PACIFICORPâ€™s KLAMATH HYDROELECTRIC PROJECT FERC #2082 Tribal

HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 1

ATTACHMENT A

PRELIMINARY

COMMENTS and 10(a) RECOMMENDED TERMS AND CONDITIONS

for

PACIFICORP’s KLAMATH HYDROELECTRIC PROJECT

FERC #2082

By the

Tribal Fisheries Department, Hoopa Valley Tribe March 29, 2006

Hoopa, California

OVERVIEW

This document provides the Fisheries Department of the Hoopa Valley Tribe (HOOPA FISHERIES) 10(a) Recommended Terms and Conditions for relicensing of the Klamath Hydroelectric Project (Project), Federal Energy Regulatory Commission (FERC) Project No. 2082. Our comments are organized first with a section describing the authorities that guide HOOPA FISHERIES’s participation in this relicensing process, followed by comments and recommended terms and conditions for the new license for operation of the Project. These terms and conditions may be modified as needed with the issuance of the FERC Draft Environmental Impact Statement, and as new information and additional study reports from the Licensee, federal, state and tribal entities are made available during the relicensing process. HOOPA FISHERIES’s Statutes, Management Policies, and Rules for Fish and Wildlife Resources In accordance to its charge to implement the fisheries policies of the Hoopa Valley Tribe, HOOPA FISHERIES submits these recommendations to protect, conserve, and improve fish resources in the Klamath Hydroelectric Project relicensing. The Tribe is not convinced that fisheries impacts of the Project can be substantially mitigated with dams below Keno in place. Therefore, the Tribe supports removal of Project dams at Iron Gate, CopCo 1, CopCo 2, and JC Boyle HOOPA FISHERIES has authority under the laws of the Hoopa Valley Tribe and pursuant to Section 10(a) of the Federal Power Act (FPA) to provide recommended terms and conditions to the FERC regarding protection, mitigation of damages to, and enhancement of fish and wildlife and their habitat affected by operation and management of the Klamath Project. HOOPA FISHERIES’s goals and objectives for the fish and wildlife populations in the Klamath Basin are found in the following statutes and plans: The Hoopa Valley Tribe’s Fisheries Implementation Plan requires HOOPA FISHERIES to manage fish resources of the Tribe to maintain and enhance the natural resources of the Klamath Basin and to protect the natural resources of the Klamath Basin from adverse impacts caused by hydroelectric and other water management projects. Where impacts cannot be avoided, those impacts shall be mitigated. The InterTribal Fisheries Reintroduction Plan was finalized in March 2006, and awaits formal adoption of the Hoopa Valley Tribal Council. The goals for the reintroduction plan are to (1) restore native fish access to historical habitats; and (2) reestablish anadromous fish runs in the Upper Klamath Basin (the area above Iron Gate Dam [IGD], including Upper Klamath Lake [UKL] and its tributaries) that are self-sustaining and can support tribal harvest. The Tribal goal of restoring native anadromous fish to historically used habitat in the Upper Klamath Basin is generally consistent with the stated goals or objectives of federal and state resource managers, and with a HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 2

long-range plan for restoring Klamath Basin fisheries that a multi-party task force completed under authority of a law passed by the U.S. Congress in 1986 (P.L. 99-552). Water quality conditions in the lower mainstem Klamath River below Iron Gate Dam are a widespread concern and will ultimately affect the degree to which any reintroduction program within the upper basin will be successful. Poor lower river conditions related to environmental degradation associated with the Project are affecting the suitability of existing mainstem conditions for salmon. This situation affects existing runs of fish in the mid-Klamath basin, and will affect any future upper basin runs unless remediated. Together, these statutes, rules and plans set forth the Hoopa Valley Tribe’s comprehensive plan and standards that HOOPA FISHERIES has used to develop its 10(a) recommendations. The fundamental principle behind these recommendations is to ensure that Tribal fish and wildlife resources are holistically managed to not only maintain or enhance vital Tribal resources, but also protect these resources from adverse impacts caused by the continued existence of a project.

These statutes, rules, and plans are provided to FERC to assist with its development of protection, mitigation and enhancement measures for the new Project license. In addition to FERC’s duties under Section 10(a), Section 10(a) of the Federal Power Act requires FERC to consider “the extent to which a project is consistent with a comprehensive plan for improving, developing or conserving a waterway affected by the project.” HOOPA FISHERIES respectfully requests that FERC consider these standards and plans in preparation of the Environmental Impact Statement (EIS) for a new hydroelectric license.

INTRODUCTION General The original federal and state license and state water right and power claims for the Klamath Hydroelectric Project were issued without consideration for conservation of affected natural resources and without due consideration for the federal fiduciary duties to tribal trust resources. The Project’s Construction and ongoing operation and maintenance have adversely affected fish and their habitat. The Final License Application (FLA) submitted by the Licensee on February 28, 2004 to FERC contains minimal provisions to protect, conserve, or enhance fish and wildlife resources. Project Description The Klamath Hydroelectric Project is located on the upper Klamath River in Klamath County of south-central Oregon, and in Siskyou County of north-central California. The Project has six mainstem hydroelectric developments between river mile (RM) 190 and RM 254, a re-regulation dam with no generation facilities, and one tributary hydroelectric development on Fall Creek. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 3

Indigenous Fish Populations Spring-run, and winter-run steelhead Oncorhynchus mykiss, spring and fall Chinook Oncorhynchus tshawtscha, coho Onchorhynchus kitsutch, and Pacific lamprey Lampetra tridentata were extirpated from their historical range in the upper Klamath River basin and its associated tributaries (Fishpro 2000) when Copco 1 and 2 dams were constructed in 1917 without fish ladders, and then at a later date, Iron Gate Dam was constructed downstream from Copco 1 without fish ladders. The Klamath Hydroelectric Project blocks passage of native anadromous fish to 65% of the Klamath basin. A review of historic distribution indicates that anadromous fish once occupied over 300 miles of habitat that is now blocked by the Klamath hydroproject. The Klamath River historically had the third largest salmon runs on the Pacific Coast of North America, after the Columbia and Sacramento rivers. HOOPA FISHERIES’s goal for Klamath River fish populations is to restore the native, indigenous species to levels existing immediately prior to the construction of the Klamath Hydroelectric Project. Native resident fish in the vicinity of the Project include redband (rainbow) trout, and two species listed by the federal Endangered Species Act (ESA) as Threatened, the shortnose sucker Chasmistes brevirostris, and Lost River sucker Deltistes luxatus. Relicensing Summary The Project is owned and operated by PacifiCorp under a single FERC license (No. 2082), issued in1956 by the FERC. The existing license expired March 1, 2006. PacifiCorp initiated formal FERC relicensing in December 2000 when it filed a Notice of Intent and First Stage Consultation Document (FSCD) to relicense the project. The Licensee has followed FERC’s Traditional Relicensing Approach and initiated a “Plus” process of consultation with state, federal, and tribal agencies and other stakeholders. HOOPA FISHERIES provided comments on the FSCD in March 2001 and subsequent study proposals in later letters and emails. The Licensee conducted studies and filed its DLA on June 24, 2003. HOOPA FISHERIES provided comments on the DLA to PacifiCorp on September 17, 2003. In its review of the DLA, HOOPA FISHERIES found that The Applicant failed to provide requested information. In some cases, field studies and data analysis were not completed. In other cases, the Licensee either chose not to conduct recommended studies, or chose not to use methodologies as recommended. The Licensee also did not propose protection, or mitigation and enhancement measures (PMEs) to mitigate for project impacts in the new license period as required by 18 CFR 16.8 Identification of Protection, Mitigation and Enhancement measures. HOOPA FISHERIES concluded that the DLA was incomplete The FLA, submitted to FERC in February 2004, was required to address study deficiencies, determine appropriate PME types and scale, and present conclusions of comprehensive studies that were requested by HOOPA FISHERIES and other participants, including description of the scope, methods, results, and analysis of such HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 4

studies. Similar to the DLA, the FLA was incomplete and lacked completed studies and descriptions of current conditions, Project impacts, and PM&E’s. FERC issued a series of Additional Information Requests (AIRs) on February 17, 2005, to PacifiCorp, requiring complete information from fish passage, water quality and instream flow studies. Some of these studies have been completed while for others, such as the fish passage study the AIRs are still pending. The Final License Application As described by FERC regulations (18 CFR 4.51), the purpose of the FLA is to fully disclose effects of the Project on the environment, provide sufficient information for FERC to meet its tribal trust responsibilities, obligations under the National Environmental Policy Act (NEPA) and the Endangered Species Act (ESA), and propose protection, mitigation and enhancement measures (PMEs) that will mitigate for Project impacts. The FLA is required to completely describe current conditions and Project impacts, address study deficiencies, determine appropriate PME types and scale, and present conclusions of comprehensive studies that have been requested by HOOPA FISHERIES and other participants, including description of the scope, methods, results, and analysis of such studies. Final License Application Deficiencies During relicensing consultation, The Licensee modified the formal traditional process by adding an informal collaborative process with HOOPA FISHERIES and other stakeholders including tribal, state and federal agencies and non-governmental organizations (NGOs). The informal collaborative process, called the Klamath Collaborative, was to develop, conduct, and evaluate studies in order to establish a complete technical and scientific record necessary for analyzing impacts and developing license terms and conditions, PMEs, and agency recommendations. HOOPA FISHERIES met numerous times with the Applicant and other stakeholders to resolve disagreement, develop study plans, and gather important information for the relicensing. HOOPA FISHERIES supported the Klamath Collaborative process. However, of the many aquatic and fish passage study plans developed by PacifiCorp, only three were approved by the Aquatics and Fish Passage Work Groups because major disagreements prevented stakeholders from approving study plans (FLA Exhibit E 4-139). In response, The Licensee split studies into smaller proposals where stakeholders could live with individual pieces. For example, documenting impacts of peaking at JC Boyle Peaking Reach became a mix of three approved study plans, three unapproved study plans and others as incomplete concepts. The Licensee supplied thousands of pages in its FLA and subsequent responses to FERC’s AIR. However, the FLA and AIR responses fail to fully describe and quantify Project impacts. Since the Licensee minimized the scope of important studies or simply HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 5

declined to do several studies, other parties (e.g., the Environmental Protection Agency, the North Coast Regional Water Quality Control Board, the Oregon Department of Environmental Quality and the Klamath Tribes) have funded additional data collection and analyses. As a consequence, development of a comprehensive administrative record describing Project impacts to aquatic and riparian resources is still pending. We appreciate the AIRs that FERC requested of PacifiCorp on February 17, 2005, since a complete technical and scientific record was not assembled in the FLA. However, while results have been submitted in the past several months from the fish passage, water quality and instream flow studies, and despite these studies’ results, there is a lack of significant PME’s to address Project impacts. Discrepancies of fact have not been resolved, differences in interpretation of study results remain, and results and conclusions based on independent analysis contradict the Licensee’s study conclusions. Because of these discrepancies of facts, conclusions and independent analysis, HOOPA FISHERIES submits to FERC 10(a) recommendations to avoid or minimize the risks of Project impacts to fish and wildlife populations to the greatest extent possible and to ensure resource goals and objectives and state statutory requirements are met. Removal of Keno Dam and Riverine Reach from the FERC Project Boundary The Licensee has proposed to remove Keno Dam from the FERC project boundary in the FLA as is reflected in the REA, which only includes the Project proposal submitted by PacifiCorp to FERC. HOOPA FISHERIES contends that Keno Dam and the river reach below should remain in the FERC boundary since it continues to be owned and managed by the Licensee for re-regulating flows to maximize peaking and power generation at downstream dams including JC Boyle, and Copco 1 and 2. HOOPA FISHERIES recognizes that Keno Dam also facilitates management of water for the US Bureau of Reclamation (USBR) irrigation project. The Licensee originally included Keno Dam and the river reach within the project boundary in its DLA. The purpose of Keno Dam in the DLA included flow regulation for hydroelectric power. The Licensee now proposes to eliminate Keno Dam from the Project boundary in the FLA apparently to avoid responsibility for mitigation of the dam’s substantial impacts to fish, wildlife and water resources, such as lack of effective upstream and downstream fish passage that FERC, HOOPA FISHERIES and other agencies can recommend or require. The Licensee contends that USBR operations are the driving force affecting flows at Keno when spill conditions are not occurring. The USBR hydrologist for analyzed input and output flows when spill is not occurring at Keno Dam, as well as Link River, Lost River and irrigation project net diversions. He determined that the Licensee’s fluctuations in Keno releases are a result of refill needs at the JC Boyle reservoir and not irrigation project operations (September 6, 2005 email from John Hicks to David Diamond). The analysis indicates that there appears to be little relationship between Keno flows and the daily change in irrigation operations, and on some days, they move HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 6

opposite to how irrigation operations should affect Keno releases. Based upon these data, HOOPA FISHERIES believes that the Licensee’s management of Keno flow releases are a direct result of refill needs to maximize generation at the three peaking facilities, JC Boyle and Copco 1and 2 dams, and not irrigation project operations. Keno Dam causes major water quality problems to the Klamath River (Deas 2003, 2004). Water quality modeling and data indicates that Keno Dam negatively affects water quality parameters by storing water, increasing retention time and solar exposure, thereby contributing to problems related to temperature, dissolved oxygen, pH, un-ionized ammonia, and nutrient dynamics. Deas (2003) documented that Keno Reservoir has very poor water quality conditions, dominated by a large standing crop of phytoplankton. During spring and summer the reservoir experiences extreme persistent anoxia, elevated nutrient conditions, high sediment oxygen demand, and heavy thermal loading. These degraded water quality impacts can be measured over 200 miles downstream, and adversely affect upstream and downstream fish passage. Given that Keno facilities and operations are used for flow regulation for hydropower generation, and given their impacts, HOOPA FISHERIES opposes the Licensee’s proposal to remove Keno Dam and its river reach from the Project boundary. The 10(a) recommendations below include conditions for the Keno portion of the Project. Resource Concerns for the Relicensing of the Klamath Hydroelectric Project HOOPA FISHERIES’s primary concern is to ensure that adequate mitigation is provided for ongoing and in some cases unavoidable losses of habitat caused by the Project. The Project causes many impacts to fish and wildlife resources and their habitats within the Project area and downstream along the Klamath River. These impacts are briefly summarized and include but are not limited to the following: 1) Fish Passage: The Project has several impacts to upstream passage at Project facilities, including Iron Gate, CopCo 1, CopCo 2, JC Boyle and Keno dams. There are no fish passage facilities at Project facilities located downstream from Keno Dam. With regard to downstream fish passage and entrainment in power canals, there are no screens at Eastside and Westside diversions at Link River Dam, or at Copco 1, Copco 2, and Iron Gate diversion intakes. JC Boyle intake is screened but not to current state and federal design standards. Currently, the majority of downstream migrating fish are diverted through unscreened or inefficiently screened diversions and into powerhouse turbines. More than 300 miles of migration, spawning, and rearing habitat for salmon, steelhead, and Pacific lamprey are no longer accessible due to the construction and operation of the California dams of the Klamath Project. Lack of fish passage facilities at Copco 1, Copco 2, and Iron Gate Dams has blocked passage to the upper basin, which encompasses 65% of the total Klamath River Basin area. All species of anadromous fish in the Klamath Basin have been on a general decline for much of the past century. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 7

The decline of the anadromous fish in the Klamath Basin coincides with the construction and operation of the Project. 2) Fish Resources: Existing operating conditions and facilities cause impacts to fish populations by blocking or impeding migrations, reducing stream flows below levels required to support habitat of vital significance, by fluctuating stream flow, which causes mortality of fish by stranding and severely limits productivity of channels, by entraining fish into power diversions, and by adversely affecting water quality within and downstream from the Project. PacifiCorp is proposing to adjust the Project boundary to exclude the Keno Dam, which will limit the scope of analyzing project effects on fish populations. Based on HOOPA FISHERIES Research staff and other sources, the Project’s impacts to fish resources include, but are not limited to:

Blockage of habitats above and within the Project necessary for survival, growth and reproduction of native anadromous fishes including Pacific lamprey, Chinook salmon, Coho salmon and Steelhead

Negative impacts to water temperatures in the Klamath River below Iron Gate Dam during critical periods in spring and fall.

Exclusion of native anadromous fish from refugial habitat within and above the Project.

Water quality impacts to the Klamath River below Iron Gate Dam related to populations of highly toxic blue green algae.

Reduced and degraded fish habitat in the JC Boyle and Copco bypass reaches, and in the JC Boyle peaking reach.

Continued loss of fish habitat inundated by JC Boyle, Copco, and Iron Gate reservoirs.

Delayed upstream migration of redband trout past the JC Boyle facilities. Depleted prey and macroinvertebrate sources within bypass and peaking

reaches. Stranding and mortality of juvenile salmonids in the JC Boyle peaking reach Loss or alteration of spawning and rearing habitat as a consequence of peaking

operations. Impediments to upstream migration that result in increased susceptibility to

disease, reduced metabolic efficiency, and reduced reproductive potential. Barriers to upstream migration and downstream recruitment of trout. Enhanced habitat for non-native fish that compete with native species for forage

and habitat in Project reservoirs. Reduced habitat and degraded water quality for native non-anadromous fish

species as a function of inadequate minimum flows downstream of JC Boyle Dam.

Habitat loss and degradation because of diversions and lack of fish ladders and screens on Spring Creek.

Massive, repeated fish die-offs from Keno Reservoir downstream to Topsy Reservoir due to poor water quality in Keno Reservoir.


Decreased fish health and size in the JC Boyle peaking and bypass reaches. Lack of habitat for redband trout fry and native minnow species in the JC Boyle

peaking reach. 3) Flow Fluctuations and Minimum Flows: Impacts caused by flow fluctuations vary with timing (seasonal, night, and day), magnitude, duration, and frequency, which reduces aquatic habitat, strands fish on shorelines, reduces spawning success, reduces important stream edge habitat, and reduces production capacity for aquatic species. Peaking also causes bank erosion and has affected the extent and character of riparian vegetation. The Project impacts approximately 45 miles of Klamath River within Oregon, and the entire length of the river within California. Low flows and high ramping rates affect both bypass reaches and peaking reaches below dams where flow is regulated. There are no FERC mandated minimum streamflow requirements in Project bypass reaches except in the JC Boyle bypass reach for 100 cubic feet per second (cfs), and the Copco 2 bypass reach for 10 cfs in. Low stream flows reduce available fish habitat and exacerbate water quality problems. During most of the year, from JC Boyle powerhouse to Iron Gate Dam, river flows are diverted through powerhouse turbines. In the case of JC Boyle and Copco 2 facilities, these flow diversions result in largely dewatered segments of the river, or bypasses, between the dam and the powerhouse, with the majority of water diverted to penstock intakes and turbines. JC Boyle releases approximately 80-100 cfs through screen bypasses and the fish ladder. The majority of water is directed to the penstock intakes. Fish that enter the JC Boyle and Copco 2 bypass reaches below the JC Boyle and Copco 2 dams face substantially altered river characteristics. In addition, flow diversion and peaking operations have altered hydrologic conditions in the Klamath River, affecting the hydrology between JC Boyle and Iron Gate Dams and portions of Fall Creek, Spring Creek, and Jenny Creek. The proposed boundary adjustment by the Licensee would eliminate analysis of Project-affected reaches from Link River Dam to the JC Boyle Powerhouse. The following summarize impacts in bypass and peaking reaches:

Diversion of flows from the JC Boyle bypass reach (100 to 2,850 cfs) reduces flows in the upstream portion of the bypass by 75% to 97% and with addition of natural springs of approximately 220 cfs, reduces flows in the downstream portion of the bypass reach by 48% to 90%.

The magnitude, frequency, and duration of peak flows (seasonal high flows) in the JC Boyle bypass reach are reduced as a result of Project operations.

The seasonal and annual variability of flow in the JC Boyle bypass reach is reduced as a result of Project operations.

Project operations reduce summer daily minimum flows (40 to 60%) in the JC Boyle peaking reach, exceeding impacts described in the FLA.

Project operations increase summer daily maximum flows in the JC Boyle peaking reach.


Project operations divert 98 to 99.5% of flow from the Copco 2 bypass reach except during peak flows in excess of 3,200 cfs.

The Spring Creek diversion reduces flows in Spring and Jenny creeks. Fall Creek flows are reduced by the Fall Creek diversion.

In the absence of meaningful PMEs, these Project impacts will continue to degrade aquatic and riparian habitat and water quality and prevent achievement of HOOPA FISHERIES management objectives for restoration of riverine habitat for fish species. 4) Water Quality: The Klamath River suffers from very poor water quality in part attributable to the Project. From its headwaters at Upper Klamath Lake to its mouth at the Pacific Ocean, the States of Oregon and California identify the Klamath River as water quality limited under Section 303(d) of the federal Clean Water Act. Warm water temperatures and enriched nutrient conditions, particularly during the summer and early-fall months, plague the river system and affect fish, aquatic organisms, and other designated beneficial uses of the waters. Data and modeling results from the water quality re-licensing studies indicate that Project dams including Keno, JC Boyle, Copco 1, and Iron Gate, negatively affect water quality parameters by storing water and increasing retention time and thermal exposure, thereby contributing to water quality problems related to temperature, dissolved oxygen, and nutrient dynamics. Reduced flows in the JC Boyle bypass reach cause seasonally increased warming and rates of warming upstream of the springs and colder stream temperatures downstream of the springs to the powerhouse. The FLA does not include an adequate and comprehensive discussion of Project impacts on water quality and beneficial uses. Since FERC requested completion of the water quality studies in an AIR request, some information has become available. The water quality modeling results and hydrologic data has been difficult to assess within the set of CDs released by the Licensee; therefore it is impossible to fully validate the Licensee’s conclusions regarding the impact of Project operations on water quality. However, despite the lack of a completely transparent process and analysis, the current data appear to indicate that Project operations alter water quality for temperature, dissolved oxygen (DO) and nutrient cycling within and downstream of Project reservoirs and in river reaches subject to diversion and peaking operations, as well as in Spring, Fall and Jenny creeks. 5) Cumulative Impacts: The incremental impact of the Project and other land and water use practices, such as alteration of the natural hydrology, on the environment was not analyzed in the FLA. Cumulative effects can result from individually minor, but collectively significant impacts occurring over the lifetime of the Project. While there are many different land and water management activities that have contributed to the decline of the Klamath River fishery and habitat, construction of the Licensee’s hydroelectric Project stands out as the most direct and detrimental of all the activities. The combination of lack of fish passage, peaking, loss of contact of the river with a


native, riparian zone, lack of sediment recruitment, and degraded water quality has led to the steady decline of native fish and wildlife populations. 6) Restoration: The Licensee has not proposed PMEs to address near-term habitat restoration. Failure to mitigate for these impacts will continue the associated disruption of natural ecological relationships that leads to habitat loss, habitat fragmentation, and biological resources loss, as well as causing an overall drop in fish and wildlife production. FERC has authority to require mitigation of this type that enhances fish and wildlife resources to reduce negative impacts attributable to a project since its construction, as confirmed in American Rivers et al. v. FERC, 187 F.3d 1007 (9th Cir. 1999). Species that show a declining trend in populations include wild spring chinook, wild steelhead, wild fall chinook, and Pacific lamprey, while wild coho in the Lower Klamath River are listed as a federally threatened species. HOOPA FISHERIES believes the Licensee should provide additional mitigation in the form of specific habitat mitigation projects or, in the alternative, establish a fund that will be used to develop additional habitat mitigation. The scope of the Licensee’s commitment should include acquisition of in-stream water rights or flows, critical riparian/riverine reserves and refugia, and passage and screening at non-project facilities. Continued inundation of key historic spawning habitats cannot be replaced by passage facilities that, even if reasonably effective, will cause mortality via reservoir predation and capturing and handling mortality of both adults and juveniles, delayed migration, and loss of production capacity in the upper basin. Continued operation of the Project will limit anadromous fish production unless the new license includes a combination of fish passage and habitat restoration. It should be noted that a license term greater than 30 years might reduce financial risk for the operators, but increases the risk that mitigation measures will not be sufficient to deal with project impacts over the next license period. Public values will change during the next 30-50 years. As an example, the last 50 years included major federal legislation such as the Clean Water Act and Endangered Species Act, which reflected a shift in recognition of public resource values. In addition, unidentified and unforeseen impacts will occur, such as future listing of additional species. For these reasons, it is of particular importance that the Licensee provides sufficient mitigation for the Project.

10(a) RECOMMENDED TERMS AND CONDITIONS HOOPA FISHERIES provides the following terms and conditions pursuant to Federal Power Act, 16 USC 803(a). HOOPA FISHERIES will submit revised 10(a) recommendations, that may reflect updated information, following 45 days of the issuance of the DEIS. Development of these terms and conditions has been coordinated with the Tribal Environmental Protection Agency, which has primary responsibility for implementing tribal regulatory authority delegated from the Federal Government pursuant to the Clean Water Act. These recommended terms and conditions have been coordinated with HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 11

other state and federal agency stakeholders including the California Department of Fish and Game (CDF&G), California State Water Resources Control Board (CSWRCB), US Fish and Wildlife Service (USFWS), US National Marine Fisheries Service (NMFS), US Bureau of Land Management (BLM), US Forest Service (USFS), US Department of Interior (DOI), USBR, US Bureau of Indian Affairs (BIA), and US National Park Service (NPS). These recommended terms and conditions have also been shared with entities including representatives of the Klamath, Yurok, Karuk and Tribes, as well as with interested stakeholders. Recommended license terms and conditions are set forth below in italics, followed by a discussion of the issue and rationale for each recommendation.

1. Resource Management Plans, Annual Reports, and Monitoring And Compliance Reports

1A. Resource Management Plans. Within one year of license issuance, the Licensee shall develop and submit to FERC for approval Resource Management Plans for 1) Project Operations, 2) Water Quality, 3) Fish Passage, 4) Sediment and Gravel, 5) Wildlife Mitigation, 6) Fish and Wildlife Habitat Restoration, and 7) Vegetation and Noxious Weed Management to direct and guide implementation of HOOPA FISHERIES 10(a) license conditions and other agency resource conditions over the term of the license and any subsequent annual licenses. These Resource Management Plans shall be proposed as a part of the first Annual Report submitted within one year of license issuance. The Licensee shall consult in the formulation of the resource plans with resource staff from HOOPA FISHERIES and other state, federal and tribal resource agencies and the Resource Management Plans shall be reviewed and approved by HOOPA FISHERIES and other state, federal, and tribal stakeholders. The Resource Management Plans shall be updated every 5 years with consultation and approval from HOOPA FISHERIES and other resource agencies to reflect new information, new management needs, and updated implementation strategies. 1B. Annual Reports. For the term of the license and any subsequent annual licenses, the Licensee shall annually submit to the FERC, HOOPA FISHERIES and other state, federal and tribal agencies an Annual Report to ensure resource management consistent with the HOOPA FISHERIES 10(a) license conditions. The Annual Report shall consist of an the Annual Work Plan for the upcoming year, and a narrative summary and associated tables and graph where appropriate, of completed implementation for the previous year of resource plans for Project Operations, Water Quality, Fish Passage, Fish and Wildlife Habitat Restoration, Sediment and Gravel, Wildlife Mitigation, Vegetation and Noxious Weed, and Monitoring and Compliance Reports. Each of these sections of the Annual Report shall be developed according to procedures set out in these license conditions, and any specific requirements included in other agency license conditions (i.e. section 18 requirements for fish passage).


1C. Consultation on Resource Plans. The Licensee shall prepare each Resource Plan after consultation with HOOPA FISHERIES. The Licensee shall allow a minimum of 60 days for HOOPA FISHERIES to comment and make recommendations prior to filing the plan with the Commission. The Licensee shall include with the plan documentation of consultation and copies of comments and recommendations on the completed plan after it has been prepared and provided to HOOPA FISHERIES, and specific descriptions of how HOOPA FISHERIES’s comments are accommodated by the plan. The Licensee shall implement the approved Resource Plans. 1D. Monitoring and Compliance Reports. As a part of the Annual Reports, the Licensee shall submit Monitoring and Compliance Reports for each of the seven resource plans. Monitoring and Compliance Reports shall provide specific information regarding compliance with the section 10(a) license conditions, and short and long term monitoring of activities conducted pursuant to the section 10(a) license conditions. Monitoring and Compliance Reports are required for each resource plan: 1. Project Operations. A report with narrative and graphs summarizing an annual compilation of the monthly information. Condition 10.

• Daily Project inflow; • Graphical plots of hourly data below the Link River, Keno and JC Boyle dams

and JC Boyle powerhouse; • A graphical plot of hourly ramping rates; and • An annual summary of Non-Compliance Reports.

2. Water Quality. A report with narrative and graphs summarizing data demonstrating compliance with water quality requirements and standards for Project reservoirs and reaches, and an annual summary of Non-Compliance Reports. Condition 8.

• Water temperature; • Dissolved oxygen (DO); • Total Dissolved Gas (TDG); • pH; • Chlorophyll a; • Nutrients including nitrogen, phosphorus; • Toxic Algae; and • An annual summary of Non-Compliance Reports.

3. Fish Passage. A report with narrative and graphs summarizing an annual compilation and summary of the activities associated with implementation and monitoring of fish passage: Items shall include evaluation of passage options and improvements, monitoring of biological, water quality and hydraulic criteria for upstream and downstream passage facilities, and a report of upgrades and improvements where performance measures are met and not met. Conditions 3 and 4.


4. Sediment and Gravel. A report with narrative and graphs summarizing an annual compilation of activities associated with mitigation and restoration measures and associated monitoring that shall be implemented to mitigate for the lack of sediment transport through Project reaches to riverine habitat. Condition 9. 5. Wildlife Mitigation. A report with narrative and graphs summarizing an annual compilation of information and data for wildlife mitigation measures including a) Raptor Protection for monitoring raptor injury and mortality at power poles and implementation of protection devices, and b) Wildlife Entrapment and Mortality to monitor and implement wildlife protection at power canals and other project features. Condition 11. 6. Fish and Wildlife Habitat Enhancement. A report with narrative and compilation of information summarizing progress toward restoring fish and wildlife habitat within the Project area, below, within and above the Project area. Condition 12. 7. Vegetation and Noxious Weed Management. A report with narrative and compilation of information, data and graphs summarizing progress toward implementation of strategies for managing native vegetation to optimize habitat for wildlife species and control invasive weed species. Condition 12. Issue and Rationale Resource management plans are needed to provide a framework and guidance to bring the Project up to current environmental standards and to provide an opportunity for the Licensee to consult with FERC, and HOOPA FISHERIES and the other state, federal and tribal agencies on development and implementation of resource plans. Under the existing license, there is little to no tracking of impacts of Project facilities and operations to natural resources. With the onset of the re-licensing process, very little historical data had been compiled by the Licensee to assess Project effects. The re-licensing process has strongly illuminated the need to build a series of implementation plans to guide Project implementation of PMES along with an interactive and functional process of coordination and communication between the Licensee and resource agencies. Annual monitoring and reporting is needed to organize Project implementation activities, resource management information, promote resource goals, and ensure compliance with HOOPA FISHERIES’s section 10(a) recommendations for license conditions and other resource agency conditions adopted into the new license. The annual reporting and planning process provides HOOPA FISHERIES and other regulatory agencies a means of overseeing and tracking the Licensee’s compliance with the agency conditions and provides a process to implement adaptive management during the term of the license where needed. This condition also structures management and reporting requirements for the convenience of the Licensee.


The Klamath Hydroelectric Project has had issues of non compliance with respect to some resources such as upstream and downstream fish passage at JC Boyle Dam in the JC Boyle peaking reach. Development and implementation of resource plans and annual monitoring and compliance reporting will provide a means for resource agencies to bring information forward to the Licensee and FERC when concerns for impacts to resources arise in the new license.

2. Consultation Requirement 2A. Consultation Requirement. The Licensee shall provide a minimum of a 60-day notice, and opportunity for HOOPA FISHERIES and other state, federal and tribal stakeholders to provide review and comment on all plans and actions required by license conditions. Consultation shall be documented in each plan or report submitted to the Commission. Issue and Rationale Fish and wildlife resources under the jurisdiction of HOOPA FISHERIES are impacted, both directly and indirectly, by the operation of the Project. The Project impoundments are located upon private and federal lands and directly impacts riparian and wetland resources, shorelines, water quality, native fish and wildlife populations, and their habitats. HOOPA FISHERIES has developed recommended license conditions and prescriptions, which it has concluded, are necessary to address these impacts and provide for the protection and utilization of these resources. To assist the Licensee in developing plans and reports that appropriately address the Project’s impacts to these natural resources it is necessary for the Licensee to engage HOOPA FISHERIES and other state, federal and tribal stakeholders in consultation regarding the fulfillment of these section 10(a) license conditions, and other license prescriptions proposed by other agencies.

3. Upstream Fish Passage Facilities

3A. Upstream Passage at Oregon Klamath Hydroelectric Dams, Keno and JC Boyle dams. The Licensee shall provide for the safe, timely, and effective upstream passage of Chinook and coho salmon, steelhead trout, Pacific lamprey, and redband trout and federally listed suckers. The Licensee shall construct, operate, maintain, and evaluate volitional fishways at JC Boyle and Keno dams. The ladders shall provide for the uninterrupted passage of fish over the full range of river flows for which the Project maintains operational control. The ladders shall have a minimum of two entrances and associated entrance pools. The auxiliary water system (AWS) shall be designed to augment ladder flow from the forebay. The ladder entrances shall be located downstream of the fish screen bypass outfall (JC Boyle) and any existing velocity barriers below the existing ladder entrances. The AWS shall be screened in accordance with NMFS juvenile fish screen criteria or such alternative criteria as may be determined acceptable by HOOPA FISHERIES, NOAA, and USFWS. The AWS shall be designed to provide the correct water temperature and water quality as to HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 15

attract fish. The fish ladders and AWS together must supply at least 5-10 percent of high fish passage design flow for adequate attraction to the ladder. The maximum slope of the fish ladders shall not exceed 10 percent at JC Boyle Dam and 4 percent at Keno Dam. The fishways shall be constructed and operational within 4 years for Keno Dam and 5 years for JC Boyle Dam of the effective date of the new license. The Licensee shall, within two years of license issuance and in consultation with the HOOPA FISHERIES, develop detailed design and construction plans of the ladders for review and approval by the HOOPA FISHERIES, NMFS, USFWS and CDFG prior to construction. The design shall include features to hold, and sort fish by age and species. The Licensee shall provide designs, and upon resource agency approval, construct volitional upstream fish passage (ladders) at Keno and JC Boyle dams. The ladders must meet federal and state performance standards and criteria for juvenile and adult rainbow trout and also meet criteria for anadromous fish including Chinook salmon, Coho salmon, steelhead, and Pacific lamprey and federally listed species of the shortnose and Lost River suckers. The Licensee shall provide a minimum of 60 days for HOOPA FISHERIES and affected agencies to review and comment on the fishway design and construction plans. The Licensee shall implement any design modifications necessary for the upstream movement of fish as required by HOOPA FISHERIES. The HOOPA FISHERIES-approved designs shall be filed with FERC. Construction of fish passage facilities at the Keno and JC Boyle dams must be completed within 4 and 5 years, respectively, following issuance of the new FERC license. The Licensee shall, prior to the completion of construction of the new fishways, and in consultation with HOOPA FISHERIES and affected agencies, develop a post-construction monitoring and evaluation plan to assess the effectiveness of the fishway. The plan shall include hydraulic, water quality, and biological evaluations to assess the performance of the fishway, including measures for follow-up evaluations of fishway effectiveness. Specific biological performance parameters shall include the number of fish, by species, size, and age class, and observed at each facility. The Licensee shall keep a record of the daily observations by a qualified fisheries biologist on the physical condition of the fish using the fishways. Water quality parameters shall include a continuous record of DO and water temperature at locations in the fishway as determined by HOOPA FISHERIES and affected agencies and in front of and adjacent to the entrance(s) and exit(s) of the fishways. The evaluation plan and the results of effectiveness monitoring shall be provided to HOOPA FISHERIES and affected agencies for review and comment, with a minimum of a 60-day review period. The Licensee shall implement any plan modifications, operational or physical changes necessary for the safe, effective, and timely passage of fish as may be required by HOOPA FISHERIES and affected agencies. Hydraulic evaluation of each facility shall be initiated within one month following construction completion. Biological evaluation shall be initiated within a timeframe established through consultation with HOOPA FISHERIES and affected agencies that will consider the timing and magnitude of potential fish migration.


Biological evaluations shall be accomplished with either visual monitoring equipment or installation of a fish trap and counting system. The Licensee shall purchase, and replace when needed, the necessary equipment to monitor fish passage. The Licensee shall promptly provide fish passage records to HOOPA FISHERIES upon request. 3B. Upstream Passage at California Klamath Hydroelectric Project dams, and Spring and Fall Creek diversions. The Licensee shall provide designs and construct, upon HOOPA FISHERIES approval, volitional upstream fish passage at Copco 1, Copco 2 and Iron Gate dams, and Spring and Fall Creek diversions. The ladders must meet federal and state performance standards and criteria for juvenile and adult rainbow trout, and also meet criteria for anadromous fish including Chinook and Coho salmon, steelhead, and Pacific lamprey for Copco 1 and 2 dams and Iron Gate Dam, and juvenile and adult rainbow trout at Spring and Fall Creek diversions. Criteria for passage of Pacific lamprey are detailed in Attachment B, Lamprey Passage Recommendations for the Klamath River. Construction of fish passage facilities at the Copco 1 and 2 and Iron Gate dams must be completed within 5 years following license issuance while the fish passage facilities for Spring and Fall Creek diversions must be completed within 5 years following issuance of the new FERC license. The Licensee shall, prior to the completion of construction of the new fishways, in consultation with HOOPA FISHERIES and affected agencies, develop a post-construction monitoring and evaluation plan to assess the effectiveness of the fishway. The plan shall include hydraulic, water quality, and biological evaluations to assess the performance of the fishway, including measures for follow-up evaluations of fishway effectiveness. Biological evaluations shall be accomplished with either visual monitoring equipment or installation of a fish trap and counting system. The Licensee shall purchase, and replace when needed, the necessary equipment to monitor fish passage. The Licensee shall promptly provide fish passage records to HOOPA FISHERIES upon request. Specific biological performance parameters shall include the number of fish, by species, size, and age class, and observed at each facility. The Licensees shall keep a record of the daily observations by a qualified fisheries biologist on the physical condition of the fish using the fishways. Water quality parameters shall include a continuous record of DO and water temperature at locations in the fishway as determined by HOOPA FISHERIES and affected agencies, and in front of and adjacent to the entrance(s) and exit(s) of the fishways. The evaluation plan and the results of effectiveness monitoring shall be provided to HOOPA FISHERIES and affected agencies for review and comment, with a minimum of a 60-day review period. The Licensee shall implement any plan modifications, operational or physical changes necessary for the safe, effective, and timely passage of fish as may be required by HOOPA FISHERIES and affected agencies. Hydraulic evaluation of each facility shall be initiated within one month following construction completion. Biological evaluation shall be initiated within a timeframe established through consultation with HOOPA


FISHERIES and affected agencies, considering the timing and magnitude of potential fish migration. 3C. Submittal of Draft Designs. The Licensee shall submit draft design plans to HOOPA FISHERIES and affected agencies within three years following license issuance HOOPA FISHERIES approval of design specifications for upstream fish passage facilities. The Licensee, after consultation with HOOPA FISHERIES and affected agencies and within six months from the start of construction shall file for Commission approval functional design drawings of the upstream fish passage facilities. 3D. Performance Standards. In the event that the Licensee proposes upstream facilities that do not meet extant federal and state criteria, the Licensee shall design, construct, test, operate, and maintain upstream fish passage that meets the performance standards set forth in the following table. Performance Standards for Klamath Hydroelectric Project Fish LaddersPassage Component Measures of Success

Upstream Passage Survival at each Klamath Hydroelectric Project facility/reservoir

> 95 % adult survival during first 5 years of operations.

> 98 % adult survival after 5 years.

The criteria contained in Table 3D will be applied as follows: 1. Design and build the facility to achieve the adult survival rate. 2. Test the facility hydraulically and biologically to optimize performance for 5 years after construction. 3. If after 5 years, test results indicate that adult survival rates associated with the ladder fall within the range of values contained in the table above, no additional modifications are required. 4. If test results indicate that injury and mortality rates fall below the range of values contained in the table above, the Licensee will undertake minor additional modifications to reduce injury and mortality rates. However, if after 2 years of additional testing, minor additional modifications achieve the adult survival rates identified above, and adult survival rates fall within the range of values above, no major modifications are required.

5. If test results then indicate that adult survival rates associated with the facility again fall below the table, undertake major operational or structural modifications to reduce injury and mortality. 6. If test results after major operational or structural modifications to reduce injury and mortality cannot meet performance objectives within 10 years of license issuance, the Licensee shall construct volitional passage facilities as prescribed by law. 3E. Post Construction Evaluation and Improvements. In the event that performance standards in Table 3D are not met during the post construction evaluation period, the Licensee shall implement changes to Project operations or facilities at any facility not meeting the performance standards within a time frame established by HOOPA HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 18

FISHERIES and affected agencies and developed through consultation with the Licensee. Measures to bring the fish passage facilities into compliance with performance standards at each facility may include, but are not limited to, the following: (1) improved hydraulic balancing of ladder cells or structural modifications, (2) construction of additional upstream fish passage facilities, (3) seasonal changes in operations to facilitate upstream fish passage, and (4) reductions in flow diversions. 3G. Written Operation and Maintenance Procedures. The Licensee shall develop written standard operation and maintenance procedures (including operator training and supervision) to ensure that the upstream fish passage facilities operate effectively during the life of the project. The operation and maintenance plan shall include procedures for prior notification and coordination with HOOPA FISHERIES and affected agencies on maintenance scheduling or emergencies that affect functioning of the facilities. The operation and maintenance plan shall include measures for daily inspections for staff gage readings and obstructions during the peak seasonal migration of major species including redband trout, suckers and anadromous fish, and weekly inspections during non-peak migrations. 3H. Post Construction Monitoring Plan. Prior to completion of the upstream fish facilities, the Licensee, in consultation with HOOPA FISHERIES and affected agencies, will prepare a written post-construction monitoring plan and implementation schedule to evaluate the efficiency and biological effectiveness of the facilities. The plan shall incorporate recommendations by HOOPA FISHERIES and affected agencies before implementation. The plan must include hydraulic and biological evaluation to ensure proper performance of the facilities as established in agency criteria. The written plan will evaluate and monitor fish movement by species and life stage immediately following construction to evaluate the fish passage facilities. The plan shall determine whether fish death, injury, or delay is occurring; and whether fish have difficulty in locating the ladder entrances, moving through the ladders, or falling back over the spillway on the dam. The results of the monitoring shall be submitted to the agencies according to the approved schedule. If after two years of monitoring and evaluation, the results of the monitoring show that modifications to the facilities are necessary to eliminate or minimize adverse impacts to the fish resources, the Licensee shall file with the Commission recommendations for modifying the facilities and a schedule for implementing the measures that shall incorporate agency recommendations developed through consultation. Measures to bring the ladders into compliance with the standards may include, but are not limited to, improved hydraulic balancing of ladder cells or structural modifications, seasonal Project shutdown, or reduction in flow diversion. These changes may be required for the remaining term of the license or may be required temporarily until alternative measures are implemented to achieve the standards. 3I. Operations and Maintenance. The Licensee shall maintain all upstream fish passage facilities by keeping them in repair, operating them within federal and state criteria, and open and free from obstructions at all times, consistent with state and federal law. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 19

3J. Maintenance Shutdowns and Fish Salvages. The Licensee shall notify HOOPA FISHERIES and affected agencies at least two weeks in advance of any contemplated maintenance shutdowns that may result in dewatering the waterways or reduced flow conditions that may result in stress or mortality to fish. The Licensee shall salvage live fish from the waterways during such maintenance shutdowns and consult with HOOPA FISHERIES to determine where the salvaged fish will be relocated. 3K. Decommissioning. To the extent that agency consultations determine that it is infeasible to provide safe, timely and effective passage at any Project facility, the Licensee shall prepare a decommissioning proposal for the subject facility in consultation with state, federal and tribal stakeholders. Issue and Rationale Compliance with Law: The Klamath Hydroelectric Project is not operated in compliance with state statutes, rules, and fish management plans. The Project fishway facilities located in Oregon are ineffective and do not meet federal or state passage criteria for trout, anadromous salmonids, or native suckers and lamprey, while the California dams do not have upstream (or downstream) fish passage facilities at all. The Applicant has not proposed modifications of existing facilities or new facilities that address anadromous fish passage or proposed a consistent, comprehensive strategy for native, migratory fish passage through Project facilities. Needed upgrades at JC Boyle and Keno Dam are not proposed, and no passage facilities are proposed for Iron Gate, Copco 1, or Copco 2 dams, where native, migratory species are isolated by lack of passage. Thus, passage needs of native fish, including listed suckers, have not been adequately addressed. Fish passage recommendations are proposed at Project facilities in California to support restoration of anadromous fish to historic habitats in California and Oregon, since our interests are affected by Project facilities and operations at all Klamath Project dams. Oregon and California coastal fishers have shared a mixed stock fishery of anadromous fish originating rivers from the northern California and southern Oregon coasts for over a century. The Klamath stocks have had a very low abundance in recent years and as a weak stock, have restricted ocean fisheries for Chinook south of the Columbia River. The health of Klamath stocks affects allocation of fish resources for Oregon, Washington, California and Alaska users, as well as numerous tribes with fishing treaties with the United States government. The Klamath populations also factor into harvest allocation agreements between the United States and Canada, regulated by the Pacific Salmon Treaty. Existing Project Facilities: Existing upstream fish passage facilities at JC Boyle Dam pass some redband/rainbow trout and other fish but they are ineffective and they do not meet current passage criteria for potamodromous and anadromous fish. Passage problems may be related in part to channel degradation near the entrance of the fish ladder which occurred after dam construction (USDI 2004). The gradient that existed as part of the original fishway has not been maintained over the term of the license. Steep HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 20

gradient, attraction flow, hydraulic barriers, and problems with entrances limit the passage effectiveness of JC Boyle dam fishway. Keno Dam has a fishway that generally conforms to salmonid-based criteria but does not meet slope guidelines for sucker passage (USFWS 2005). Although it conforms to slope and energy dissipation criteria for salmonids, the Keno Dam fishway and auxiliary water supply system have attraction hydraulics and flow regulation problems. The remaining project dams and diversions including Copco 1, Copco 2, and Iron Gate dams and the Spring and Fall Creek diversions do not have upstream fish passage facilities. The Licensee has not proposed any upstream fish passage facilities at Copco 1, Copco 2, and Iron Gate dams but has proposed fish ladders for the Spring and Fall Creek diversions. The proposed ladders at the Spring and Fall Creek diversions will have pool and weir type ladders with a 0.5 foot vertical jumps. However, these facilities will need to meet all state and federal fish passage criteria Reintroduction of Anadromous Fish: Pacific lamprey, spring and fall Chinook salmon, coho salmon, and steelhead trout were present historically above the dam. Adequate passage conditions will ensure that the project does not impair future restoration of fish populations in the upper Klamath system. Fish passage through the Project for a suite of species is essential to reconnecting the system ecologically. The Klamath River once supported the third largest salmon and steelhead runs on the Pacific coast. Runs of spring and fall chinook salmon were present in upper basin tributaries to Upper Klamath Lake. Steelhead were in the mainstem river up to Link River Falls and possibly in the Upper Klamath Basin, and coho were documented in the Klamath River above Iron Gate and Copco dams. Pacific lamprey distribution is thought to have coincided with anadromous fish distribution. The Project effectively blocks access and upstream movement of salmon adults into the historic spawning areas above RM 190 and many important tributary habitats. The dams further constrain the ability of smolts and juvenile fish to migrate downstream. The present day distribution of anadromous fish in the Klamath River is restricted to below Iron Gate Dam. Coho have been listed as threatened under the Endangered Species Act. This listing along with significant declines in salmon and steelhead runs emphasize the need to provide mitigation that will increase or restore self-sustaining populations in historic ranges to ensure conservation of species. Fish passage is essential mitigation that will address the loss of natural fish production capability from historic habitat in and above the Project and loss of fish harvest opportunity from Project operations. Spring and fall runs of Chinook salmon occurred in the Sprague, Williamson, and Wood Rivers in the Upper Klamath Basin, now all rendered inaccessible to anadromous fish by the construction of Copco Dam in 1918. These rivers were important salmon spawning streams (Fortune et al. 1966; Lane and Lane Associates 1981; Hamilton et al. 2005). Steelhead trout also migrated through the Project area to upper basin HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 21

tributaries. Coho salmon and Pacific lamprey historically accessed habitat above Iron Gate Dam. Salmon passage was considerable before the 1918 completion of Copco I Dam blocked upstream fish passage in the Klamath River. During construction of the dam, the Klamath Tribes noted that salmon runs were affected, and the Vice President of the California-Oregon Power Company stated the company’s intention to provide a fish ladder at Copco I Dam. Provision of a ladder at Copco I was also consistent with the wishes of the BIA. Subsequently, however, the power company decided to build a hatchery at Fall Creek, and not to construct a fish ladder at Copco I (USDI 2004). Passage of Pacific lamprey must be accommodated through incorporation at all Project dams of fishway design criteria specific to the needs of this important fish (Steward and Associates 2006). Fishway designs based solely on needs of salmon, steelhead, trout and suckers are unlikely to provide for unique needs of lamprey during their extended freshwater life cycle, nor during migrations of smolts and spawners. Habitat Production Potential: Huntington (2004) estimated nearly 150,000 returning adult spring and fall chinook as a lower end of potential productivity and more than 6,500 returning adult steelhead if passage is provided through and above the Project (Table X). Huntington also estimated potential productivity from existing suitable habitat based on multiple, simple expansions from other data, an analysis that suggested 18,700 Chinook salmon and about 8,000 steelhead trout could result from providing passage at this time. Huntington’s estimates of potential production are based entirely on habitat potential and do not account for mortality caused by fish passage facilities at existing hydropower dams, effects of flows, poor water quality (especially temperature), and harvest. Huntington’s estimates also do not account for additional fish produced as “half pounders”, a life history produced in many southern Oregon and northern California rivers. The river above Iron Gate Dam would likely produce half pounders due to the fact that Bogus Creek steelhead have almost an 100% half pounder life history and provide a very popular fishery from Seiad Valley to the mouth of the Klamath River.


Table Preliminary estimates of current potential production and historical production (number of returning spawners) of Chinook salmon and steelhead in areas of the Klamath River Basin above Keno Dam. Data compiled from (Huntington 2004a).

Current Production Potential1

Estimated Historic Production Upstream of Upper Klamath Lake

Chinook Spawners Steelhead Spawners Geographic

Area Chinook

Spawners Steelhead Spawners Low High Low High

Williamson River 11,614 93,552 531 4,281 Sprague River 123,154 195,791 5,636 8,959 Wood River Valley 14,966 148,681 685 6,804 Total 18,704 7,966 149,734 438,024 6,852 20,044 1 adjusted for miles in Tier 2; no harvest

In the Pacific Northwest, reintroduction and/or restoration via dam removal or passage improvement efforts at FERC hydroelectric projects is underway on the Elwha, Deschutes, Lewis, Cowlitz, Skagit, Umpqua, Hood, White Salmon, Sandy, Clackamas, Willamette, and Upper Columbia rivers. There are numerous examples of successful introductions of anadromous salmonids to new habitats worldwide. Native, Resident Fish: Improved passage at the Oregon and California Project dams provides benefits to the restoration of native migratory redband trout including restoration of historical seasonal migration patters for immature fish, restoration of population connectivity and genetic diversity. The development of detailed design and construction plans in consultation with HOOPA FISHERIES and affected agencies is critical to ensure that effective passage measures are incorporated into the design. The construction timelines are necessary to meet resource goals and objectives as quickly as possible. Habitat fragmentation and degradation have been identified as the most likely limiting factors for native migratory redband trout and ESA-listed suckers in the Klamath River. With the exception of JC Boyle and Keno that have passage facilities with limited effectiveness, the five mainstem dams of the Project lack passage and have isolated potamodromous fish populations, reduced native fish abundance within some segments, and disrupted potamodromous fish movement between river segments. The JC Boyle and Keno dams have ladders with a pool and weir design. However, these ladders appear to be an obstacle to fish passage due to inadequate design. Historically, migrations of redband trout were documented throughout the Klamath River basin. Redband trout exhibit a springtime migration in the JC Boyle and Keno areas of HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 23

the river, from the Frain Ranch area at river mile (RM) 217 to Klamath Lake at RM 251, with a smaller migration during the fall (Fortune et. al. 1966). Contemporary passage continues to be less than 5-10% of that reported 1 year after project construction of JC Boyle Dam. In addition, the size of redband trout passing over the ladder showed a significant decline in length frequency of redband trout in the intervening 30 years (Buchanan et. al. 1991). Buchanan et. al. (1994) reported that the close similarity of redband trout from Spring Creek and Trout Creek (which are above Upper Klamath Lake) to Spencer Creek and the Klamath River (which are below Upper Klamath Lake) and to steelhead from Bogus Creek in California suggests that some of these lake populations were once associated with runs of anadromous rainbow trout. The ladder at JC Boyle is steeper than current HOOPA FISHERIES criteria for trout and its entrance location, flow and water quality relative to the river may provide poor attraction for upstream migrating fish. Similarly, the Keno Dam ladder configuration has a much steeper slope than the passage criteria for suckers. Sucker passage may even be more important at this ladder to reconnect endangered suckers in the Keno Reach and Topsy Reservoir to sucker habitat upstream of Keno Dam, including Upper Klamath Lake. Most of the automated weirs lack adequate orifice passage and fish using the ladder have to jump over these last four weirs to pass into the reservoir. Trapping studies indicated that trout use the ladder, but the Keno fish ladder does not meet HOOPA FISHERIES criteria for passage of trout. Locations of the entrance, weir design, flow velocity, hydraulic gradients and water quality at the JC Boyle and Keno ladders have not been evaluated by the Licensee during the relicensing process to ascertain rainbow trout, lamprey and sucker population passage needs and potential reintroduction of anadromous fish. The JC Boyle ladder is contained in License Article 32 of the existing FERC license. Future facilities will require hydraulic evaluation to determine facility effectiveness. Future facilities will also require biological evaluations to assess passage effectiveness, potential migration delays, fallback or injury, fishway entrances, ladder configurations, and velocity gradients or barriers. The Licensee will also need to further modify newly constructed facilities based on biological and hydraulic evaluation study results and agency approval, to ensure proper performance.

4. Downstream Fish Passage Facilities 4A. Downstream Passage at JC Boyle Dam. The Licensee shall provide designs, and upon HOOPA FISHERIES approval, shall construct volitional downstream fish passage at JC Boyle Dam. The Licensee shall, to provide for the safe, timely, and effective downstream passage of Chinook and coho salmon, steelhead trout, Pacific lamprey, and redband trout, as well as protection of federally listed suckers. The Licensee shall construct, operate, maintain, and evaluate a fish screen at JC Boyle Dam. The screens shall be operated year-round and shall be designed in accordance with criteria as determined by HOOPA FISHERIES and affected agencies. The screens shall provide for the uninterrupted passage of fish over the full range of river flows for HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 24

which the Project maintains operational control. Criteria for passage of Pacific lamprey are detailed in Attachment B, Lamprey Passage Recommendations for the Klamath River. Passage facilities will be designed to include a trap for evaluating screen performance and to accommodate long-term monitoring of the downstream migrant population. The screens shall divert all fish to a sorting facility, where federally listed suckers are segregated from downstream migrating fish and suckers are returned to upper JC Boyle reservoir on a daily basis. Downstream migrating fish will be delayed no longer than eight hours, with the exception that fish captured at night will be released at night, while fish captured during the daylight will be released during daylight. Construction of fish downstream fish passage facilities at JC Boyle Dam must be completed within 5 years of license issuance. Hydraulic evaluation of each facility shall be initiated within one month following construction completion. Biological evaluation shall be initiated within a timeframe established through consultation with HOOPA FISHERIES and affected agencies, considering the timing and magnitude of potential fish migration. The screen and bypass design shall meet the criteria and have fishway components designed considering the most recent National Marine Fisheries Service or US Fish and Wildlife Service fish passage criteria and guidelines for juvenile and adult redband trout, ESA-listed sucker species and Chinook salmon, Coho salmon, steelhead, and Pacific lamprey. In addition, the screen and bypass design must include adequate facilities for evaluating screen and bypass facility performance (e.g., fish trapping capability). The screen facility, where appropriate, shall include criteria also adopted by interagency agreement of HOOPA FISHERIES, USFWS, and CDFG in July 2005 for interim criteria for the upper Klamath basin. These include NMFS juvenile salmonid criteria, except in slack water where a bypass is not practical, an approach velocity of 0.2 ft/sec, or a special site agreement with the 3 fish agencies. 4B. Downstream Fish Passage at Keno Dam. Within 1 year of license issuance, the Licensee shall prepare a biological evaluation plan after consultation with HOOPA FISHERIES and affected agencies to determine safe, effective downstream fish passage over Keno Dam. Criteria for passage of Pacific lamprey are detailed in Attachment B, Lamprey Passage Recommendations for the Klamath River. The Licensee shall allow a minimum of 60 days for HOOPA FISHERIES to comment and make recommendations prior to filing the plan with the Commission. The Licensee shall include with the plan documentation of consultation and copies of comments and recommendations on the completed plan after it has been prepared and provide to HOOPA FISHERIES and affected agencies, and specific descriptions of how HOOPA FISHERIES and affected agencies’ comments are accommodated by the plan. Within 2 years of license issuance, the Licensee shall implement the approved biological evaluation plan to determine whether passing through the small gate openings of the spill gates, auxiliary water supply, or sluice conduit is harmful to HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 25

potamodromous and anadromous fish. The Licensee shall use the results of the evaluation, in consultation with HOOPA FISHERIES and affected agencies to determine whether spillway modification is necessary, and implement any necessary changes. The evaluation may be conducted by radio tagging groups of fish released upstream of the dam, setting up receiver antennas in the spill gate openings, and monitoring passage. Continued tracking shall assess mortality. The Licensee shall trap a sample of fish as they exit through the spill gates to examine fish for physical injury can assess injury. Within 4 years of license issuance, the Licensee shall implement modifications to downstream passage facilities for downstream migrating juvenile fish. 4C. Downstream Passage at California Klamath Hydroelectric Project dams and Spring and Fall Creek diversions. The Licensee shall design and construct, upon HOOPA FISHERIES and affected agencies’ approval, new screen and bypass facilities at the Klamath Project California mainstem hydroelectric facilities to provide volitional fish passage at Copco 1, Copco 2 and Iron Gate dams, and Spring and Fall Creek diversions for native potamodromous and anadromous fish species. The downstream fish passage facilities must meet performance standards and criteria established by HOOPA FISHERIES and affected agencies for juvenile and adult rainbow trout at the Spring and Fall Creek diversions, and meet criteria for anadromous fish including chinook and coho salmon, steelhead, and Pacific lamprey at the California mainstem Project dams. Criteria for passage of Pacific lamprey are detailed in Attachment B, Lamprey Passage Recommendations for the Klamath River. The Licensee shall provide designs, and upon agency approval, construct volitional downstream fish passage at the California mainstem Klamath Project dams and at the Spring and Fall Creek diversions. The Licensee shall provide for the safe, timely, and effective downstream passage of Chinook and coho salmon, steelhead trout, Pacific lamprey, and redband trout, as well as protection of federally listed suckers. The Licensee shall construct, operate, maintain, and evaluate a fish screen at the California Project dams and redband trout at the Spring and Fall Creek diversions. The screens shall be operated year-round and shall be designed in accordance with HOOPA FISHERIES juvenile fish screen criteria. The screens shall provide for the uninterrupted passage of fish over the full range of river flows for which the Project diversions maintain operational control. The screen and bypass design shall meet the criteria and have fishway components designed considering the most recent NMFS or USFWS fish passage criteria and guidelines for juvenile and adult redband trout, ESA-listed sucker species and Chinook salmon, Coho salmon, steelhead, and Pacific lamprey. Construction of the downstream fish passage facilities at the Copco 1 and 2 and Iron Gate dams must be completed within 5 years, following license issuance while the fish passage facilities for Spring and Fall Creek diversions must be completed within 5 HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 26

years following license issuance. Hydraulic evaluation of each facility shall be initiated within one month following construction completion. Passage facilities will be designed to include a trap for evaluating screen performance and to accommodate long-term monitoring of the downstream migrant population. Downstream migrating fish will be delayed no longer than eight hours, with the exception that fish captured at night will be released at night, while fish captured during the daylight will be released during daylight. Biological evaluation shall be initiated within a timeframe established through consultation with HOOPA FISHERIES and affected agencies, considering the timing and magnitude of potential fish migration by all native species. 4D. Downstream Passage at Eastside and Westside Diversions. The Licensee has proposed to decommission the Eastside and Westside diversions (FLA ES1.2.1 and 1.2.2). The Licensee shall, after consultation with HOOPA FISHERIES, prepare a Decommissioning Plan for the Eastside and Westside diversions that includes permanent sealing of the intakes and fish-proofing potential areas of mortality or injury. The Licensee shall allow a minimum of 60 days for HOOPA FISHERIES and affected agencies to comment and make recommendations prior to filing the plan with the Commission. The Licensee shall include with the Decommissioning Plan documentation of consultation and copies of comments and recommendations on the completed plan after it has been prepared and provided to HOOPA FISHERIES and affected agencies, and specific descriptions of how HOOPA FISHERIES and affected agencies’ comments are accommodated by the plan. Within one year of license issuance, the Licensee shall submit the Decommissioning Plan to the Commission for approval. The Licensee shall implement the Decommissioning Plan within one year of approval by the Commission. 4E. Submittal of Draft Designs. The Licensee shall, within two years of the effective date of the new license and in consultation with HOOPA FISHERIES and affected agencies, develop detailed design and construction plans for review and approval by HOOPA FISHERIES and affected agencies prior to construction. The design shall include features to hold, sort fish by age and species for the safe, effective, and timely passage of fish. Criteria for passage of Pacific lamprey are detailed in Attachment B, Lamprey Passage Recommendations for the Klamath River. The Licensee shall provide a minimum of 60 days for HOOPA FISHERIES and affected agencies to review and comment on the fish screen design and construction plans. The Licensee shall implement any design modifications necessary for the downstream movement of fish as required by HOOPA FISHERIES and affected agencies. The agency approved designs shall be filed with the Commission. The Licensee, after consultation with HOOPA FISHERIES and affected agencies and within six months from the start of construction shall file for Commission approval functional design drawings of the downstream fish passage facilities.


4F. Performance Standards. The Licensee shall design, construct, test, operate, and maintain fish screen(s) that meets the criteria set forth in OAR 635-412-0010-0040. In lieu of such post-construction performance standards set forth in Table 4F below, PacifiCorp may satisfy its obligations with respect to fish screens by constructing fish screens to NMFS design criteria dated January 1997 or the draft version from January 2004(?) or the most current revision of those criteria, as appropriate. Table 4F.Performance Standards for Klamath Hydroelectric Project Fish ScreensSmolts > 60 mm in Length Fry < 60 mm in Length Mortality Injury Mortality Injury Design performance objective < 0.5% mortality

Design performance objective < 2% injury

Design performance objective < 2% mortality

Design performance objective < 4% injury

Actual mortality ≥ 0.5% but < 2% would require additional work to lessen mortality

Actual injuries ≥2% but < 4% would require additional work to lessen injuries

Actual mortality ≥ 2% but < 4% would require additional work to lessen mortality

Actual injuries ≥4% but < 6% would require additional work to lessen injuries

Actual mortality ≥ 2% would require major operational or structural changes

Actual injuries ≥4% would require major operational or structural changes

Actual mortality ≥4% would require major operational or structural changes

Actual injuries ≥6% would require major operational or structural changes

The criteria contained in Table 4F will be applied as follows: 1. Design and build the screen to achieve injury and mortality rates contained in the first horizontal row of the table. 2. Test the screen hydraulically and balance the screen to optimize performance. 3. Test the screen biologically. If test results indicate that injury and mortality rates associated with the screen fall within the range of values contained in the first horizontal row of the table, no additional modifications to the screen are required. 4. If test results indicate that injury and mortality rates fall within the range of values contained in the second horizontal row of the table, undertake minor additional modifications to reduce injury and mortality rates. The objective of such modifications is to achieve the injury and mortality rates contained in the first horizontal row of the table. However, if minor additional modifications fail to achieve the injury and mortality rates contained in the first horizontal row of the table, but injury and mortality rates fall within the range of values contained in the second horizontal row of the table, no major modifications are required.

5. If test results indicate that injury and mortality rates associated with the screen fall within the range of values contained in the third horizontal row of the table, undertake major operational or structural modifications to reduce injury. 6. If test results after major operational or structural modifications to reduce injury and mortality cannot meet performance objectives within 10 years of license issuance, the


Licensee shall construct volitional passage facilities as prescribed in OAR 635-412-0010-0040. 4G. Post Construction Evaluation and Improvements. In the event that performance standards in Table 4F are not met during the post construction evaluation period, the Licensee shall implement changes to Project operations or facilities at any facility not meeting the performance standards within a time frame established by HOOPA FISHERIES and affected agencies and developed through consultation with the Licensee. Measures to bring the screens into compliance with performance standards at each facility may include, but are not limited to, the following: (1) improved hydraulic balancing of screens or structural modifications, (2) construction of additional screening facilities, (3) seasonal shutdowns of turbines, and (4) reductions in flow diversions. 4H. Written Operation and Maintenance Procedures. The Licensee shall develop written standard operation and maintenance procedures (including operator training and supervision) to insure that the downstream fish passage facilities operate effectively during the life of the project. The operation and maintenance plan shall include procedures for prior notification and coordination with HOOPA FISHERIES and affected agencies on maintenance scheduling or emergencies that affect functioning of the facilities. The operation and maintenance plan shall include measures for daily inspections of downstream fish passage facilities for staff gage readings and obstructions during the peak seasonal migration of major species including redband trout, suckers and anadromous fish, and weekly inspections during non-peak migrations. 4I. Post Construction Monitoring Plan. The Licensee shall, prior to the completion of construction of the new fishways, in consultation with HOOPA FISHERIES and affected agencies, develop a post-construction monitoring and evaluation plan to assess the effectiveness of the fishway. The plan shall include hydraulic, water quality, and biological evaluations to assess the performance of the fishway, including measures for follow-up evaluations of fishway effectiveness. The plan will guide monitoring activities immediately following construction to evaluate the fish passage facilities. The plan shall determine whether fish death, injury, or delay is occurring, and whether fish have difficulty in locating the screen and bypass facilities. The plan must include the estimation, through statistical sampling, the number of fish, by species, size, and age class, observed at each facility and a record of the daily observations by a qualified fisheries biologist on the physical condition of the fish using the fishways. The plan must also include provisions for documentation of a continuous record of DO and water temperature within the fishways at locations to be determined by HOOPA FISHERIES and affected agencies, and in front of and adjacent to the entrance(s) and exit(s) of the fishways. The evaluation plan and the results of effectiveness monitoring shall be provided to HOOPA FISHERIES and affected agencies for review and comment. At least 60 days shall be provided for review. The Licensee shall implement any plan modifications, operational or physical changes necessary for the safe, effective, and timely passage of fish as may be required by HOOPA FISHERIES and affected agencies. The results of the monitoring shall be submitted to the agencies according to HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 29

the approved schedule. If the results of the monitoring show that modifications to the facilities are necessary to eliminate or minimize adverse impacts to the fish resources, the Licensee shall file with the Commission recommendations for modifying the facilities and a schedule for implementing the measures that shall incorporate agency recommendations developed through consultation. Measures to bring the screens and bypass facilities into compliance with the standards may include, but are not limited to, improved hydraulic balancing, structural modifications, seasonal Project shutdown, or reduction in flow diversion. These changes may be required for the remaining term of the license or may be required temporarily until alternative measures are implemented to achieve the standards. 4J. Operations and Maintenance. The Licensee shall maintain all downstream fish passage facilities by keeping them in repair, and open and free from obstructions at all times, consistent with state and federal law. 4K. Maintenance Shutdowns and Fish Salvages. The Licensee shall notify HOOPA FISHERIES and affected agencies at least two weeks in advance of any contemplated maintenance shutdowns that may result in dewatering the fishways or reduced flow conditions that may result in stress or mortality to fish. The Licensee shall salvage live fish from the waterways during such maintenance shutdowns and consult with state and federal agencies to determine where the salvaged fish will be relocated. 4L. Decommissioning. To the extent that agency consultations determine that it is infeasible to provide safe, timely and effective passage at any Project facility, the Licensee shall prepare a decommissioning proposal for the subject facility in consultation with state, federal and tribal stakeholders. Issue and Rationale Compliance with Law: Much of the same Issue and Rationale discussed in upstream passage recommendations applies to downstream passage as well. The Licensee does not operate the Project in compliance with HOOPA FISHERIES’s statutes, rules, and fish management plans. The JC Boyle fish screens and bypass facilities are ineffective for native trout and suckers while the Eastside and Westside diversions and California Project diversions have no screen and bypass facilities to prevent entrainment of fish. The Project entrains indigenous trout and suckers into diversion canals, depleting fish populations. Entrainment of fish into the power canals removes them from natural streams, removes them from the spawning population, causes injury and mortality by increased predation and passage through turbines, and reduces recreational opportunities. HOOPA FISHERIES has a responsibility to protect downstream migrating fish under tribal law. HOOPA FISHERIES provided screening criteria for hydroelectric projects with specific guidance and criteria on implementing screening facilities that best protect fish species. There are additional criteria to reflect the unique needs for sucker juveniles. New facilities will need to be constructed at all the Licensee diversions HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 30

Klamath Hydroelectric Project to meet the needs lamprey and suckers in the basin as well as salmonids. Existing Project Facilities: The screens that are currently installed at JC Boyle Dam do not meet current design criteria and are ineffective and there is no practical or cost-effective means to reconstruct the facilities to meet current standards to allow for more efficient fish passage. Fish protection at the Licensee’s diversions should provide at least the same level of protection as facilities recently constructed on other diversions within the basin, such as the A-Canal, 1,900 feet upstream from Link River Dam. The approach velocity at all 4 screens is 2.3 feet per second (fps), which is almost six times the modern criteria of 0.4 fps for redband trout and almost 11.5 times the interim agency criteria of 0.2 fps adopted in the upper Klamath basin for weaker swimming species including listed juvenile suckers. The existing screen bypass system, although consistent with the design one would normally expect for traveling band screens, does not meet modern design standards. The flow rate for the existing bypass is estimated at 20 cfs. High-pressure spray systems are supposed to keep the screens free of debris buildup, but chronically have debris build up which occasionally damages the screens requiring time-consuming repair with no backup screens in place during repair. Fish salvages in the JC Boyle power canal demonstrate significant impact to the redband trout and sucker populations. This is apparent in the number and size of trout and listed and unidentified suckers salvaged during canal maintenance activities with salvaged redband trout ranging in size from 50 to 300mm. PacifiCorp (1997) also reported tagging a high number of fish because of salvage operation in the canal below the dam. Salvage operations in the power canal document that fish of various species avoid the screen and bypass and are diverted with the majority of the flow to the power canal and turbines. This information clearly indicates that both small and large fish are passing through or around downstream protection screens at JC Boyle. Studies from the pilot study for radio-tracking upstream passage documented the migration of a single, 14-inch trout that passed upstream through the JC Boyle ladder and subsequently avoided the existing fish screens and migrated downstream through the power canal and turbines. Although Keno Dam is not a hydroelectric dam but a reregulating dam, downstream passage of juvenile fish is still impacted. The sluiceway intake is not screened. All other flows go through undershot radial gates and into shallow areas that may be predator holding locations. The remaining project dams and diversions including Eastside and Westside diversions, Copco 1, Copco 2, and Iron Gate dams, and the Spring and Fall Creek diversions do not have downstream fish passage facilities. The Licensee has not proposed downstream fish passage facilities at Copco 1, Copco 2, and Iron Gate dams but has proposed screens for the Spring and Fall Creek diversions. The proposed screens at the Spring and Fall Creek diversions will have diagonal-type screens with a maximum


approach velocity of 0.4 feet per second (fps) and a sweeping velocity of 2 times the approach velocity. However, these facilities will need to meet all fish passage criteria. Turbine entrainment at all Klamath Hydroelectric Project causes significant mortality to downstream migrating fish. For the facilities on the mainstem Klamath River, which lack screens and divert flow through Francis turbines, we assume a 24% average mortality based on the literature. Based on the literature and limited site specific sampling, significant numbers of native, potamodromous fish are currently entrained and killed at Project facilities. Reintroduction of Anadromous Fish: Many of the necessary components of the Klamath River ecosystem, despite degradation of habitats, appear to be present and functional, or are restorable to functional form. . Construction of effective upstream and downstream fishways on the Klamath River is consistent with this strategy. A run of over 30,000 hatchery and natural spring Chinook salmon still exists in the Trinity River and a remnant run of wild spring-run Chinook persists in the Salmon River. In the area of the Basin upstream from Iron Gate Dam, existing habitat continues to support fluvial and ad-fluvial populations of redband trout. In addition, several sources reported that significant unutilized habitat exists above the Project (Fortune et. al. 1966; National Research Council 2004). An example of performance standards in the Pacific Northwest is contained in the 1995 NMFS Biological Opinion for the Columbia River hydro projects, which had a combined downstream fish passage efficiency criteria of 80% per project and 95% per dam survival, which was adopted by the Northwest Power Planning Council Fish and Wildlife Program in 1994. Fish managers adopted this fish passage criterion in the 1980s as a way to address delayed mortality and included fish passage through non-turbine routes such as spill, sluiceways and screens. The long term fish passage efficiency standard for the Columbia River tribes is 90%, which equates to 98% per dam survival. These performance standards were updated in the 2000 NMFS Biological Opinion; the fish passage efficiency standard was changed to a direct survival standard, which is 95% per dam and 91% per project (dam and pool). This was an outcome of the survival standards developed by NMFS and the Mid-Columbia public utility districts for the Habitat Conservation Plan. For the Elwha River dams, fishery managers set a 98% passage standard for each dam as necessary to restore 5 stocks of salmon and steelhead. The downstream passage performance standards in this recommended license condition are consistent with those required for Soda Springs Dam by the FERC license for the Licensee’s North Umpqua hydroelectric project. When anadromous species are restored above Project dams, juvenile out-migrants will be particularly vulnerable to this impact. The progeny of these fish must negotiate the reservoir, the dam, powerhouse, and spillway for each Project facility during their out-migration. Volitional fish passage to a bypass around the turbine intakes will ensure that HOOPA FISHERIES meet its statutory goals and objectives for resource management. The development of detailed design and construction plans for review HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 32

and approval by HOOPA FISHERIES is essential to ensure that effective passage measures are incorporated into the design. Native, Resident Fish: Fortune et al. (1966) reported that Klamath Basin redband trout exhibit a pattern of downstream migration as fry or juveniles and return upstream as adults. Downstream migration of fry and juvenile redband/rainbow trout has been diminished either due to a population decline and/or this life history has been nearly eliminated because the fish screens at JC Boyle are inadequate and Link River, Copco 1, Copco 2, and Iron Gate facilities have no downstream fishways. Project dams have fragmented habitat, which has resulted in substantial population abundance, life history diversity, and productivity. ODFW Research staff monitored downstream movement below JC Boyle Dam to measure possible recruitment from Spencer Creek a major tributary above the Dam that provides the bulk of redband trout recruitment to the Klamath River. The Research staff concluded that the low numbers were not adequate to maintain the population in the river between JC Boyle Dam and the state line (Hemmingsen et al. 1992). While some trout recruitment from a small spawning area has been documented in the bypass reach, research personnel concluded that, based on an informal assessment of angler catches, the trout populations only appears to be sustaining a limited fishery with extremely conservative regulations of one trout per day, flies and lures only. An examination of the age distribution of fish populations in different segments of the Klamath River fragmented by JC Boyle Dam also indicate the impact of lack of adequate passage and project operations from the hydroelectric power project. Historically, the river was known for its abundant population of large redband trout that migrated throughout the length of the Klamath River drainage. Lack of adequate fish passage over JC Boyle Dam inhibits native, migratory redband trout from moving to and foraging in habitats that are more favorable. While restrictive angling regulations have been implemented in riverine reaches of the Klamath River in recognition of redband populations impacted by Project facilities and operations, significant recreational fisheries for redband trout remain popular in the Project area, as well as in Upper Klamath Lake, and its tributaries. Adequate upstream and downstream fish passage at JC Boyle Dam will result in restoring the connectivity of migratory redband populations in the mainstem Klamath River with those in Spencer Creek. Spencer Creek provides important habitat including spawning, and temperature related refugia areas for redband trout. Inadequate passage at JC Boyle Dam has impaired connectivity. The only entrainment study completed for the Klamath Hydroelectric Project was at the Eastside and Westside diversions prior to relicensing from 1997 to 1999 (Gutermuth et al. 2000). Based on entrainment indices, calculated from number of fish collected, percent of canal flow sampled and sampling efficiency, an estimated 792,000 fish passed through the Eastside powerhouse from July 1997 to October 1999. Similarly, an estimated 528,000 fish passed through the Westside powerhouse. The study HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 33

concluded that large amounts of fish were diverted, generally proportional to the volume of the flow diverted. Large amounts of juvenile and adult suckers were captured moving downstream, through the spring, and especially during late summer and early fall. Overall, Westside catch rates were very high often following re-opening of the canal after a period of closure. Sucker entrainment increased in the late summer and all fish entrainment increased with canal flows. Some redband trout were also entrained during the study although they were a small percentage of the catch.

5. Fish Passage Committee 5A. Fish Passage Committee. The Licensee shall establish a Fish Passage Committee for the purpose of guiding implementation of fish passage at Project facilities. The Fish Passage Implementation Committee shall consist of the Licensee; and to the extent of their interests in participating, the NMFS; USFWS; USFS; BIA; BLM; CDFG, CSWRCB; ODEQ; OWRD; affected Tribes including the Hupa, Klamath, Karuk and Yurok; and two representatives of NGOs. The Licensee’s development and implementation of fish passage including the fish passage resource plan, reports, facility designs, and operating and implementation plans submitted to the Fish Passage Committee pursuant to the terms of this license shall comply with these license conditions. The Licensee’s implementation of measures pursuant to this license shall be reported to the Fish Passage Committee as provided in any applicable implementation plan or license condition. Copies of all filings with the Commission following consultation with the Fish Passage Committee shall be provided to each member of the Fish Passage Committee. 5B. Consultation with the Fish Passage Committee. Unless a different time period is specifically established pursuant to another provision of this license, the Licensee shall, where consultation with the Fish Passage Committee is required, allow a minimum of 60 days for the Fish Passage Committee members to comment, work to achieve consensus, and to make recommendations before filing any study, operating or implementation plan, report, or facility design with the Commission. The Licensee shall include with the study, operating or implementation plan, report, or facility design: documentation of consultation with the Fish Passage Committee, copies of committee member comments and recommendations on the study, operating or implementation plan, report, or facility design after it has been prepared and provided to the Fish Passage Committee, and specific descriptions of how the comments are accommodated by the study, operating or implementation plan, report, or facility design. 5C. Fish Agency Authority. NMFS, USFWS, HOOPA FISHERIES, and CDFG are collectively referred to as the Fish Agencies. Each Fish Agency has separate and distinct statutory authorities and no agency is deemed, by virtue of concurrent approvals, to be sharing its statutory authority with any other agency or to be conceding that the approval of any other agency is required for exercise of that agency’s authority. Where consultation with the Fish Passage Committee and approval by the appropriate Fish Agencies pursuant to their respective statutory authorities is required, the licensees shall allow the Fish Agencies a minimum of 60 days to provide such approval prior to HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 34

submitting the final study, operating or implementation plan, report, or facility design with the Commission. If a Fish Agency disapproves a study, operating or implementation plan, report, or facility design, the licensees shall not file the disapproved study, operating or implementation plan, report, or design with the Commission until a dispute resolution process has been completed; in which case no further dispute resolution shall be required before such study, operating or implementation plan, report, or design is filed with the Commission. Issue and Rationale Establishment of a Fish Passage Committee will provide an efficient mechanism for coordinating consultation by the Licensee to ensure safe, effective upstream and downstream fish passage for native potamodromous and anadromous fish species are implemented. Decisions regarding developing the Fish Passage Plan, implementing specific measures for fish passage including considering passage options, design and specifications, and effectiveness monitoring for each species and life stage will be made in consultation with the Fish Passage Committee and, where specified, with the approval of HOOPA FISHERIES. Implementation committees have been established at other FERC projects (i.e. Pelton Round Butte, FERC #2030) to facilitate implementation of license conditions and coordination between resource agencies and the Licensee of the project. Implementation committees are particularly effective in coordinating professionals from a variety of backgrounds, such as biology, engineering, hydrology and water quality to provide a high level of expertise that, in the long run, may increase the success of fish passage programs. The Licensees will meet all reporting requirements of the new license regarding progress on fish passage implementation, in conjunction with ongoing Fish Committee activities. Nothing in the proposed Fish Passage Plan expands or diminishes any existing authority or confers approval authority or regulatory jurisdiction that does not already exist under applicable federal, state, or Tribal law. Each Fish Agency has separate and distinct statutory authorities and that no agency is deemed, by virtue of concurrent approvals, to be sharing its statutory authority with any other agency or to be conceding that the approval of any other agency is required for exercise of that agency’s authority.

6. Streamflow in Bypass, Peaking and Regulated Reaches This section is incomplete as HOOPA FISHERIES is coordinating with federal and state agencies for determining acceptable methodologies from different studies and considering a variety of options Accordingly, HOOPA FISHERIES reserves the right to prescribe streamfllow requirements. 6A. Preliminary Target Flow Requirements in Project Bypass and Regulated Reaches in the Klamath River mainstem from Keno Reservoir to Iron Gate Dam. For the protection of native fish species, the Licensee shall discharge a continuous HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 35

instantaneous minimum flow of 500 cfs or 70% of inflow to the Project, whichever is the greater rate. The allowed minimum flow shall either be the recommended minimum flow or total project inflow when the inflow is less than 500 cfs. 6B. Required Minimum Flows Below Klamath Mainstem Project Facilities. The licensee shall operate the project to provide flow releases that equal or exceed the following minimum flows for all Project-affected reaches within the Klamath River mainstem, including bypass channels:

• Below Iron Gate Dam: HOOPA FISHERIES recommends implementation of the Hardy Phase II (2001) instream flow recommendations for the Klamath River below Iron Gate. These recommendations are based on the best available information and are summarized in the table below:

Table 6B8. Minimum flow releases below Iron Gate Dam in cfs.

Month

Dry

Below Average

Average

Above Average

Wet

October 1100 1200 1470 1660 1900 November 1200 1400 1710 1970 2200 December 1300 1600 2030 2400 3500 January 1500 2000 2400 2970 4200 February 1600 2200 2720 3500 5000 March 1600 2400 3400 4300 5400 April 1600 2200 3300 4100 5200 May 1600 2100 3100 3700 4500 June 1350 1800 2300 2900 3800 July 1000 1250 1530 1970 2300 August 1000 1000 1250 1470 1800 September 1000 1100 1350 1570 1840

Water Year Types are defined by the following exceedance values for inflow at Iron Gate Dam:

Critically Dry - 90 per cent exceedance Dry - 70 per cent exceedance Average - 50 per cent exceedance Wet - 30 per cent exceedance Extremely Wet - 10 per cent exceedance

6B. Gages for Monitoring Streamflow. Within six months after license issuance, the Licensee shall measure and record inflow above all Project reservoirs or diversions, and outflow below each Project dam. These records shall be made available to the Tribal, Federal and State resource agencies upon request as defined in the gage installation and data reporting plan. The gauging stations shall be located at the head of each bypass reach at a location determined in consultation with HOOPA FISHERIES, ODEQ, OWRD, and USGS and serve as the compliance points for ramping rates and minimum flow requirements in the bypass reaches. The gages shall measure the full range of stage and flows that may occur at each site. Gage installation shall include radio, HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 36

telephone, or other telemetry systems to provide recording and transmission of hourly streamflow data to the Klamath Project control room. The installation of the gage stations and the data acquisition shall conform to applicable United States Geological Survey (“USGS”) standards. The Licensee shall develop, in consultation with state, federal and tribal agencies, a coordinated gauge installation and data reporting plan. HOOPA FISHERIES shall review and approve the plan prior to installation of gage stations. 6C. Timing of Project Maintenance. The Licensee shall consult with state, federal, and tribal agencies to identify the preferred timing of facilities maintenance for Project bypass reaches. The Licensee shall minimize impacts in bypass reaches by planning Project maintenance and outages in one of the two following flow periods: 1) during high flow conditions so that resulting high flows will coincide with the high-flow period of the natural hydrograph identified by the agencies and to prevent water-quality standard violations or 2) during the extreme low flow period when diversion canals will be at their lowest diversion rate and may already be shut down to meet minimum stream flow requirements, thereby minimizing or eliminating resulting stream flow stage changes and any concomitant adverse effects on aquatic resources. For the latter period, the natural hydrograph is generally still dropping through July, therefore conducting maintenance which returns flow to the natural stream channel from August 1 through September 30 will minimize stream flow changes, which will allow rainbow trout fry an additional month of growth and may reduce impacts on trout fry newly emerged in July, and will allow for a two-month window for maintenance. Resulting changes in stream flow in the bypass reaches are subject to ramping requirements. The Licensee may perform maintenance required by operating emergencies beyond its control at any time to remedy the emergency. Upon completion of emergency maintenance, ramping is subject to the ramping restrictions. The timing of maintenance activities that do not result in returning flows to natural stream channels are not limited by this recommendation. 6D. Instream Flow and Instream Habitat Enhancement Program to Mitigate for Cumulative Impacts to Aquatic and Riverine Resources. As part of Project-related mitigation for cumulative impacts, the Licensee, in consultation with state, federal, and tribal stakeholders, shall identify and fund instream flow and habitat enhancement measures in mainstem reaches and tributaries containing native fish and wildlife species. These measures shall focus on appropriate reaches within and above the Klamath Hydroelectric Project. These shall include PM&Es such as instream flow restoration, land acquisition, and working with other cooperative landowners on land and water management improvement projects to improve instream habitat. This measure is further defined and explained in the Fish and Wildlife Habitat Enhancement Plan (License Condition 12A). HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 37

Issue and Rationale Compliance with Management Direction, Administrative Rules and Basin Plans: Tribal law and HOOPA FISHERIES Implementation Plan direct staff to restore natural flow conditions in order to support ecological processes critical to fish habitat. The intent of these flow recommendations is to provide flows sufficient to allow native species, including salmon, to flourish. Project Impacts: Establishing minimum flows in bypass and other project-affected reaches is a critical component to the physical and ecological processes that influence aquatic and riparian habitat conditions in the Klamath River. Flow restoration will sustain healthy river conditions, supporting habitats to which the native aquatic and riparian communities are adapted. Under the present license, the Licensee is entitled to divert almost all stream flow from the Link River, Klamath River and Fall Creek, during much of the year except during seasonal high flows. Frequent flow oscillations in the Keno Reach and daily peaking in the JC Boyle impact cause significant variation in stream flows, negatively impacting for aquatic organisms. Therefore, much of the natural streambed is exposed or rendered marginal for support of aquatic life. A small amount of streamflow remains in the diverted, regulated and peaking reaches at a time of the year when maximum biological production should occur. The original license favored power production to the great detriment of aquatic life. To correct this imbalance, PM&Es must provide significant increases in flows through the bypass and regulated reaches. The literature consistently illustrates the adverse effect of inadequate flow on aquatic organisms. Research also indicates that beyond prescribing a minimum flow, managers should determine an appropriate flow regime based on season and water year type (Richter, B.D., et al, 1997 and Stanford, J.A., et al, 1996). The artificial manipulation of flow without reference to a baseline hydrograph can profoundly impact habitat and fish communities. The flow regime proposed by PacifiCorp perpetuates significant peaking and dewatering operations and will not protect native fish habitat from future adverse impacts. HOOPA FISHERIES concurs with the Instream Flow Council policy statement that recommends flow prescriptions to provide inter- and intra-annual variable flow patterns that mimic the natural hydrograph. The Project’s manipulation of flows beyond the magnitude, duration, frequency, or season found in unimpaired systems disrupts ecological processes and degrades aquatic habitat. Periodic disturbances such as flood and drought are inherent in natural systems. However, unnatural manipulations beyond the range of normal variation overwhelm the resiliency of native species and reduce productivity and survival of aquatic life. Native species evolved in an environment with natural variability. Spawning, incubation and rearing of native amphibians and fish are timed to natural cycles and processes and are impacted by out of season disturbances. The abnormal fluctuation in daily and seasonal flow patterns created below hydroelectric power operations results in a host of damaging impacts to native anadromous and resident fish. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 38

The results of the two studies (BLM 2002 and PacifiCorp 2005c) conducted in the JC Boyle peaking and bypass reaches documented that almost 50 years of flow alteration has impacted fish habitat and that there is very little fry habitat now available. Because channel conditions are so impaired by flow alteration, fry is the first but not only life stage impacted. However, many of the WUA curves available from these studies demonstrated that as flow is increased, habitat increases for fry, particularly as flows reach edge habitat provided by shoreline riparian vegetation. Similarly, in the Copco 2 bypass reach, which has a regulated bypass flow of 10 cfs, decades of flow alteration have altered habitat to the detriment of native fish species. The encroachment of mature alder trees into the riverine channel reflects one aspect of these impacts. PacifiCorp conducted instream flow studies but limited their analyses to non-anadromous species and also chose not to utilize the analytical cover algorithm recommended by agency instream flow specialists. Peaking operations below JC Boyle powerhouse scour river margins and have reduced fry habitat to virtually zero on a daily basis (BLM 2002). In the dewatered bypass reaches, flow reductions have facilitated invasion by exotic species, encroachment of riparian vegetation and transformation of a major river into a wadable stream. Due to the limited applicability of current studies to developing flow regimes for the future license, HOOPA FISHERIES concurs with other federal, state and tribal stakeholders in using other methods to develop flow recommendations. HOOPA FISHERIES recommends using a modification of the Tennant method (1976). Using this approach, HOOPA FISHERIES recommends for a flow that adopts a base flow then adds a percentage of inflow above the base flow, when available. Diversion of Instream Flows: The Licensee diverts a high proportion of the instream flow at each Project Facility:

• Link River: Diversions at Eastside and Westside appropriate up to 1200 and 250 cfs, while the bypass flow is 90 cfs below Link River Dam. Since the USFWS Biological Opinion was adopted for federally listed suckers in 2001, the bypass flow recommendation was increased to at least 250 cfs from June to October when needed.

• Keno Reach: Flows generally range from as low as 200 cfs up to 1700 cfs during the summer although there is no generation at Keno dam. Flows at Keno Dam are reregulated to maximize generating efficiency at JC Boyle and downstream peaking facilities and to keep the Keno pool within one foot of the high water mark to allow irrigation pumping facilities to operate. The Licensee did not conduct an instream flow study in this reach.

• JC Boyle: Diversion at JC Boyle Dam appropriates up to 3,000 cfs while the bypass flow is 100 cfs below the Dam. Spring inflow approximately half way down the bypass reach adds an additional 220 cfs for a total discharge of approximately 320 cfs from the bypass reach.

• Copco 1: Diversion at Copco 1 is 100% of the instream flow below 3,200 cfs.


• Copco 2: Diversion at Copco 2 is 97% of the instream flow below 3,200 cfs. The bypass flow is 10 cfs below Copco 2.

• Fall Creek: The Licensee’s diversion on Fall Creek has a 50 cfs capacity and only 0.5 cfs bypass requirement. The Licensee diverts 99 % of the streamflow except during the infrequent and brief storm events when flows exceed 50 cfs.

• Spring Creek: Diversion at Spring Creek is 16.5 cfs to augment flows into Fall Creek hydroelectric plant. Approximately 0.22 cfs is bypassed into Spring Creek.

• Iron Gate: Diversion at Iron Gate Dam is 100% below 1,735 cfs. Flows in excess of 1,735 cfs are spilled.

Reduction of stream flows undermines ecological processes critical to river health, and adversely affects fish resources. The Project has altered the natural flow regime in the bypass reaches and current minimum flows do not provide adequate flow for fish and other aquatic organisms. Instream flows are recommended in all Project-affected reaches to protect and restore native fish species including salmon, move the reaches toward a more natural flow regime, and restore and reconnect riparian, wetland and aquatic species. Rationale for Project Reach Flow Recommendations: Project diversions, regulation and peaking significantly reduces or fluctuates flow throughout the year in approximately 35 miles of reaches on the Link and Klamath rivers, and Fall Creek. The following bullets explain the rationale for higher minimum flows requested for each reach.

• Link River Bypass: The Link River currently has a 90 cfs minimum below Link River Dam although flows as low as 25 cfs have been observed. The recommended flow is based on HOOPA FISHERIES analysis of flows needed in support of tribal trust resources. The 2001 Biological Opinion flows of at least 250 cfs are not inconsistent with this flow recommendation as they were the best estimates of flows available, in the absence of an instream flow study that could be provided during summer months during critical water quality episodes associated with high water temperatures and low dissolved oxygen.

• Keno Reach: The Keno Reach has flow alterations in the summer that range

from 250 cfs to 1700 cfs. The existing minimum flow agreement in the Keno Reach is 200 cfs, incorporated into the current FERC license per Article 58. However, flows from 200 to 250 cfs have resulted in fish kills during hot summer conditions, as recently as June 2003. The Applicant was requested by several agencies, including HOOPA FISHERIES, to conduct a flow study in this regulated reach, but did not choose to conduct the study using standard methodology. The Keno Reach is most similar in gradient to the Caldera/Hells Corner area of the “Lower Reach”, although in many places, the Caldera exhibits a more hydraulically complex channel than the Keno Reach. With its wider channel shape and overall characteristics, it is unreasonable to expect that the


Keno Reach would require less water than the “Lower Reach” of the Peaking segment of the Klamath River.

JC Boyle Bypass Reach: The JC Boyle Bypass reach currently has a minimum

flow of 100 cfs below the dam, although half way through the reach it is augmented by spring flow.

JC Boyle Peaking Reach: The JC Boyle Peaking reach has daily flow

fluctuations of 320 cfs to as much as 3,320 cfs, a 10 fold variation in daily flow.

• Copco 2 Bypass Reach: The existing minimum flow for the Copco 2 Bypass Reach is 10 cfs, from leakage and a minor fish bypass pipe.

• Below Iron Gate Dam: Below Iron Gate dam, the FERC minimum release flows

are: 1,300 cfs from September to April, 1,000 cfs in May and August, and 710 cfs in June and July. However, since 1997, USBR’s annual project operations plans for the irrigation project in the upper basin have prescribed instream flow releases below Iron Gate Dam. These flows are dictated by the estimated amount of storage and flow based on water year type. However, these instream flows could be as low as 500-600 cfs in June, July and August, depending on the water year type. At these FERC minimum and recent USBR flows, mortality for juvenile and returning adult salmonid is regularly recorded. The conditions that killed some 70,000 adult salmon in the Lower Klamath River in September 2002 was strongly attributed to low stream flows, high water temperatures and diseases exacerbated by stream temperature and flow.

Four studies suggest a range of flow recommendations to support salmon, steelhead and other native fish below Iron Gate Dam:

1. Biologists with the CDFG conducted habitat measurements and visual estimates

and concluded that any reduction in discharge below about 1,000 cfs would lead to a diminished fishery (Wales 1944). Wales (1944) also noted that any reduction in flows below 2,000 CFS, as measured around Fall Creek, would be expected to materially affect salmon and steelhead populations downstream to the Shasta River. In 1955, a CDFG biologist estimated that 1,000 CFS provided year-round would be required to maintain game fish at 1955 levels (Sletteland 1995).

2. Trihey and Associates (1996) recommended higher summer flows than the IGD

FERC license minimums, as these additional flows are expected to “(1) reduce the growth of aquatic plants and algae, (2) provide additional wetted and surface turbulence in riffles, and (3) provide a larger volume of water in the river channel to decrease the amplitude of daily stream temperature cycles.” Trihey and Associates (1996) employed a modified Tennant (1976) method and used 60% percent of the average pre-Project annual stream flow volume and the recommended minimum IGD release schedule was “shaped” to more closely


resemble the pre-Project hydrograph. The recommended monthly instream requirements for Tribal Trust species were estimated to be: 1,200 CFS in October, 1,500 CFS between November and March, 2,000 CFS in April, 2,500 CFS in May, 1,700 CFS in June, and 1,000 CFS between July and September.

3. More recently, the Institute for Natural Systems Engineering (INSE 1999) (Hardy

Phase I study) estimated flows needed to meet the requirements of salmon and steelhead. Results of two techniques, hydrology-based methods and field-based methods, were averaged. The resulting flow regime was forwarded as an interim recommendation, until additional analyses can be completed. The INSE (1999) recommended the following interim monthly instream flows below IGD: 1,476cfs, 1,688cfs, 2,082cfs, 2,421cfs, 3,008cfs, 3,073cfs, 3,307cfs, 3,056cfs, 2,249cfs, 1,714cfs, 1,346cfs, and 1,395cfs, during October through September, respectively.

4. The most recent instream flow study results for the Lower Klamath River are from

the Hardy Phase II report. HOOPA FISHERIES recommends releases at each point of Project control to produce flows comparable with Hardy Phase II recommendations for the mainstem portions impacted by the Project.

The Hardy Phase II report recommends minimum instream monthly flows at Iron Gate Dam for 90, 70, 50, 30 and 10 percent exceedance ranges corresponding to the USBR of Dry, Below Average, Average, Above Average and Wet water year types. These flows are represented in Table 6B8 and form the basis for the HOOPA FISHERIES flow recommendation below Iron Gate dam. The purpose of providing these flows is to protect, mitigate and enhance the aquatic and riparian resources in the Klamath River impacted by the Project dams and operations.

Cumulative Impacts to Fish and Aquatic Resources: Several resident fish of the Klamath River such as redband trout are unique, as they have adapted to water temperatures ranging from 00F to 270F, extremely alkaline pH, and high nutrient levels (Behnke 1992). Prior to the construction of JC Boyle Dam in the late 1950s, the Klamath River wild trout population was noted for its abundance and large fish. Trout migrated freely through all reaches to spawn in Spencer Creek, a principal tributary of the Klamath River. Spawning likely occurred in lower gradient reaches of the river such as the areas now inundated by JC Boyle and Copco reservoirs. Endangered Shortnose and Lost River suckers, endemic to the Klamath River Basin, were once extremely abundant, and represented an important food source for tribal and recreational fishermen. They are also an important indicator of the aquatic health of the basin. However, the combination of altered seasonal and daily hydrology, ramp rates that cause direct and indirect mortality, the slowing and storing of warm, nutrient-rich waters, and fragmentation of habitat by impassable dams, has reduced habitat quantity and quality. Native fish are now faced with increased nutrient loading, more extreme, fluctuating habitat conditions and water quality, and limited ability to move between seasonal habitats. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 42

In recent years, documentation of fish kills from flow fluctuations and violations of water quality standards has demonstrated the impacts of the Project on fish populations. In June 2003, a scheduled general maintenance event at JC Boyle facilities resulted in flows being reduced to 250 cfs in the Keno Reach, causing a substantial fish kill from the extreme downramp rate and high water temperature conditions. The fish kill of more than 30,000 adult salmon in September 2002 due to low flows and high temperatures also document changes in hydrology and water quality that affect aquatic life and may be partially attributable to low flow releases at Iron Gate Dam. While flow diversion and management in the upper basin directly contributed to the fish mortality, the retention time of water in Klamath hydroelectric reservoirs may have exacerbated thermal warming to the river below Iron Gate Dam. The Licensee was able to briefly send water downstream from Iron Gate dam to assist in alleviating the situation; however, this event documents the need to incorporate flow management strategies for future operations into the new FERC license. In recognition of these cumulative impacts, the Licensee, in consultation with state, federal, tribal and NGO stakeholders should identify and fund instream flow and habitat enhancement measures in mainstem reaches and tributaries containing native fish and wildlife species within and above the Klamath Hydroelectric Project. These should include PM&Es such as instream flow restoration, land acquisition, and working with other cooperative landowners on land and water management improvement projects to improve instream habitat. Project Maintenance and Shut Downs: When routine maintenance of Project turbines occurs, all or a portion of the Project diversion capacity is typically discharged into the bypass reaches. Turbine maintenance results in a temporary, and substantial, increase in bypass reach flow that is, in most cases, not currently under any ramp rate restriction. The timing of these artificial and sudden high flow events can influence aquatic species. Conducting annual maintenance during periods when high flows would have occurred under pre-Project conditions is the most effective means of limiting negative ecological effects related to releasing full flows in bypass reaches, because native species that are present in the affected reaches are adapted to high flows during such periods. During maintenance activities when turbines are not operating, or when less than full diversion capacity can be used, headgates should be closed at each point of diversion to maintain full streamflow in the respective bypass reach.

7. Ramp Rates 7A. Ramping Rate Restrictions. During times of the year when native, migratory, potamodromous salmonid fry (<60 mm) and ESA-listed sucker juveniles are present (from approximately May 1 – September 30), ramp rates shall not exceed 0.1 feet per hour any time of the day or night in the bypass, peaking or regulated full-flow reaches below Project dams and powerhouses. During times of the year when trout fry are not present (from approximately October 1 to April 30), ramping shall not exceed 0.2 feet per hour. Ramp rates shall apply to all hydroelectric flow-regulated operations including load following, reregulating, and Project start-up and planned project shutdowns. In HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 43

addition, when anadromous fish fry are present outside the May 1 to September 30 dates listed above, ramp rates shall be limited to no ramping during the day and a maximum of 0.2 feet per hour at night. 7B. Flow Continuation Measure. Within one year of license issuance, the Licensee shall implement a flow continuation measure at the JC Boyle canal and powerhouse to provide several hours of continuous flow under powerhouse shutdown conditions. Additional project reaches will be considered for this measure as well. Issue and Rationale Compliance with Management Direction, Administrative Rules and Basin Plans: HOOPA FISHERIES’s goals and objectives for the Klamath River fish populations are to maintain and restore habitat including instream flows and natural hydrology to support healthy native aquatic species including indigenous trout, sucker, lamprey and anadromous salmonids. Habitat parameters must remain within the range that maintains the biological and requirements to support productivity, growth, reproduction, and migration of native fish. Fish survival, growth, and egg incubation and emergence are related to quantity and quality of habitat, so if the Project impacts these parameters, fish populations and their health are affected. Effects of Ramping: Project ramping occurs when operations require an increase or decrease in flow through the turbines to adjust for shifts in power demand. Ramping also occurs during project drawdown for flood control, as well as when outflow is reduced to facilitate reservoir refill. Ramping can also occur when maintenance activities require lowering Project reservoirs to access structures. Unplanned outages are an uncontrollable cause of project ramping. Project start-up after planned and unplanned outages also involves ramping. Sudden flow changes in stream reaches due to Project operations can adversely impact fish and aquatic resources. Significant rapid flow reduction in bypass, peaking and regulated reaches affect a fish population by dewatering redds and stranding fry or juvenile fish. Rapid flow increases in bypass, peaking and regulated reaches can wash out existing redds, displace fry, displace macroinvertebrates, or adversely impact amphibian populations in these reaches. Down ramping of only 1 inch per hour can impact fish populations. One very significant ramping event at a very unusual time can cause a significant limiting condition for one or more age classes of fish, or a section of habitat to be impacted for a long period (Hunter 1992). Large flow fluctuations can also result in increased erosion of important small substrate such as gravel and small cobble, which can reduce available habitat for spawning fish and macroinvertebrate species. HOOPA FISHERIES identified in comments on the DLA that the Licensee did not adequately address the effects of daily ramping and peaking operations on substrate, channel morphology and riparian shoreline habitats in the Klamath River. Daily and hourly flow fluctuations may increase the rate of erosion of shallow shoreline habitats, and with the cumulative effect of sediment recruitment HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 44

blocked by dams, magnifying the affect on aquatic, terrestrial, riparian, botanical and recreational resources. Peaking studies conducted by the Licensee were a scattered examination of different resources, with no complete analytical study. Given the lack of an integrated site-specific analysis, we refer to the literature as well as those portions of the Licensee work, which have linkage to ecological processes. Downstream dewatering and desiccation of spawning habitat were documented in the JC Boyle peaking reach (City of Klamath Falls 1986) and larval stranding was documented in a previous study. Other supporting evidence is the FERC 1990 Final EIS for the proposed Salt Caves Project that noted low adult trout densities in the upper end of the peaking reach. The EIS reported that trout in the upper peaking reach, where peaking impacts would be most visible, had relatively low growth rates and that large trout were under represented in the age structure. The EIS cited 5 years of investigation compiled by the City of Klamath Falls. The FERC EIS concluded that flow fluctuations below the JC Boyle powerhouse caused chronic stress on trout and stranding of eggs, fry, and juveniles. Stress occurred from daily flow fluctuations and related changes in water temperature and water quality. These flow fluctuations caused trout to continue to seek new feeding and resting habitat while water temperature changed metabolism and feeding rates. One of the most thorough studies of the effects of hydropower fluctuation on fish habitat was conducted in 2003 and 2004 by federal, state, tribal and private researchers in the Hanford reach of the Columbia River near Richland, Washington. The study integrated hydrodynamic modeling and Geographic Information System analyses with empirical physical and biological data. This study documented that flow fluctuations from hydropower operations caused significant mortality in juvenile fall Chinook. The following excerpt documents the relative impact of peaking operations:

“Although rearing habitat varies with streamflow, stability is likely more important to juvenile Chinook than absolute flow level. Stable flows and habitat conditions require less movement and less energy expenditure than constantly fluctuating flows and spatially variable habitat conditions. Stable flows would also help to reduce the potential for stranding or entrapment of juveniles.” (page 3).

The Hanford study on stranding and entrapment also provided insight into the stranding component of the Licensee’s peaking analysis. The Hanford researchers stated that low fish sampling probabilities confounded earlier efforts to quantify stranding and entrapment:

“…most important, the sampling approach had problems with detecting stranded fish. Fish stranded on substrates within the Hanford Reach are inherently difficult to find (i.e. detectability is low, even when fish are present). On larger substrates fish tend to migrate downwards as water recedes, requiring excavation of the site to locate dead fish. On finer substrates, fish are exposed to predators and are


often quickly removed. Because of the problems with detection of stranded fish, the estimates of stranding and entrapment impacts are likely biased low.” (page 57).

The Hanford study focused on entrapped fish to counter the sampling bias inherent in surveys for stranded fry. These entrapped fish remained visible in isolated pools or channels longer, facilitating a more accurate count. However, while these fish may not die from outright desiccation, these fish are significantly impacted by predation and thermal mortality. The Licensee’s stranding and entrapment study are consistent with the findings from the Hanford study. Field surveys were unable to detect stranded trout fry and yielded small numbers of stranded sculpin, suckers and dace and are consistent with the low numbers of trout fry rearing within the peaking reach and the poor success of visual detection methods for stranded fish. However, examination of isolated pools and side channels found trapped trout fry, larval suckers and dace. Contrary to resource agency interpretation, the Licensee discounted these observations, since fish were not technically stranded and generally still alive. A different interpretation by federal and state agencies including HOOPA FISHERIES is that fish populations are severely impacted by flow fluctuations since chronic stranding, and desiccation, predator and thermal mortality occur as result. The low abundance of fry in the JC Boyle peaking reach, that have a limited swimming ability, appears to be directly related to flow fluctuations that dramatically change available habitat by the hour. The bioenergetics analyses performed by Utah State University for the Licensee for the Project area best summarizes an assessment of peaking impacts. This study assessed bioenergetics and trout growth based on empirical data from the Boyle peaking, Boyle bypass and Keno reaches. The bioenergetics foraging model compared trout growth under existing peaking conditions and two hypothetical scenarios: without-project and run-of-the-river. The predicted trout growth for both non-peaking scenarios significantly exceeded growth under existing conditions. These results support the findings from Hanford that instability of flow translates into a significant energetic cost for fish.

Many hydropower facilities limit ramping rates to reduce the impact of stranding and entrapment. Hunter (1992) recommends a ramp rate of one inch per hour when salmonid fry are present. Based on the periodicity information provided by the Licensee on the suite of native salmonids, fry are either emerging or rearing in the Klamath River below Iron Gate Dam every month of the year, and from March to August in the Keno, JC Boyle bypass and JC Boyle peaking reaches. Ramping also impacts water quality in the peaking reach. The City of Klamath Falls (1986) documented daily temperature fluctuations of up to 120 C occur in the JC Boyle peaking reach during the middle of the summer as a result of daily peaking events, while conducting studies for the Salt Caves Project. Fredd (1991) documented temperature variations during the course of a day in the summer in the “Salt Caves reach” that varied daily from June through October from a low flow while the HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 46

powerhouse was turned off (18 hours) to approximately a one turbine peak flow of 1500-cfs (6 hours). The temperature differential, which results from this alternation of flow, was approximately 60 C daily (from 140 C to 200C on a typical summer day). Project Operations: The current FERC license does not include conditions that require the Licensee to apply specific ramping rates to operations, with the exception of the JC Boyle Peaking Reach, which has ramp rates of 9 inches per hour, and below Iron Gate Dam at 250 cfs or 3 inches per hour, which ever is less. Fish kills in the Klamath River have been documented at these high ramp rates.

• Link River Bypass Reach: The current agreement is 20 cfs/5 minutes for 0-300 cfs, 50 cfs/30 minutes for 300-500 cfs, and 100 cfs/30minutes for 500-1500 cfs. There is no formal FERC ramp rate. Fish salvages are required per the 1996 biological opinion below 300 cfs.

• Link River below the Bypass Reach: There is no formal or informal ramp rate. • Keno Reach: No FERC requirement. The Licensee indicated a self-imposed,

non-regulatory ramp rate of 500 cfs or 9 inches per hour in the FLA. This ramp rate has not been discussed or formalized with HOOPA FISHERIES or other fish management agencies. The number of hourly flow changes greater than 500 cfs per hour averages 28 for each year for water years 1995 to 2001.

• JC Boyle Bypass Reach: The Licensee’s FLA indicated a bypass reach up and

down ramp rate of 9 inches per hour. This ramp rate has not been formalized with HOOPA FISHERIES or other fish management agencies.

• JC Boyle Peaking Reach: The existing ramp rate, incorporated in the FERC

license, is an up and down ramp rate of 9 inches per hour. However, Huntington (2004) documented numerous compliance violations with some ramp rates exceeding 1.2 feet per hour for up ramping and 1.3 feet per hour for down ramping.

• Fall Creek and Spring Creek: There is no formal or informal ramp rate.

• Below Iron Gate Dam: The FERC ramp rate is 250 cfs or 3 inches per hour

whichever is less. More recently, the NMFS Biological Opinion for ESA-listed coho revised the ramp rates to 125 cfs per hour and 300 cfs per 24 hours when flows are greater than 1,750 cfs and 50 cfs per 2 hours and 150 cfs per 24 hours when flows are 1,750 cfs or less.

Project ramping occurs at the Link River, Klamath River and Fall Creek diversions when adjustments are made at the canal headgates, and at Keno Dam when flow is adjusted to re-regulate for Project operations upstream and downstream of this control point. This occurs when operations require an increase or decrease in flow in power canals for


power production or to maintain Keno Reservoir for other Project or flow operations in the basin and to accommodate irrigation interests. Ramping also occurs in these reaches when maintenance activities require dewatering or rewatering of the diversion canals. Ramping during unplanned outages occurs in the Link River, JC Boyle and Copco 2 bypass reaches of the Klamath River. For example, during an outage of the JC Boyle powerhouse, a maximum release of 3,000 cfs can occur at the emergency spillway and immediately dumps large amounts of water into the lower half of the bypass reach, augmenting flow from 320 cfs to as much as 3,000 cfs. Similarly, bringing the facility back on line, results in sudden reductions of flow in the bypass reach, as the power canal is re-watered. Ramping rates recommended by HOOPA FISHERIES are consistent with FERC conditions at other hydroelectric projects and are based on recommendations from Hunter (1992) and other ramp rates applied at hydro projects from the Pacific Northwest. The recommended ramping rates are feasible for application at the project, effective for protecting aquatic and riparian resources, and have been accepted for implementation at other hydroelectric projects by FERC. The Link River below Link River Dam and Klamath River below Keno Dam, JC Boyle Dam and JC Boyle powerhouse can be rapidly down-ramped and up-ramped during unit trips, causing both environmental and public safety concerns. FERC proposed resolving ramping issues in the Draft Environmental Impact Statement for the North Umpqua Hydroelectric Project (FERC No. 1927) as follows:

“Because many disruptions in flow result from brief turbine shutdowns (e.g., because of load rejections), hydroelectric projects should be capable of providing several hours of continuous flow under powerhouse shutdown conditions. A flow continuation measure would allow the flow regime in both the bypassed reach and downstream from the powerhouse to remain essentially unchanged during intermittent shutdown.”

A flow continuation or essentially, a synchronous bypass valve is needed to eliminate rapid water level fluctuations caused by load rejection at the Project to protect fish and wildlife and their spawning grounds and habitat caused by ramping from load rejection (see Condition 9C).

8. Project Operations and Hydrology 8A. Project Operations Plan. Within 1 year of license issuance, in consultation with HOOPA FISHERIES and affected agencies, the Licensee shall prepare a Project Operations plan to determine compliance with minimum flows and ramp rates for all Project-affected reaches. The Licensee shall allow a minimum of 60 days for HOOPA FISHERIES and affected agencies to comment and make recommendations prior to filing the plan with the Commission. The Licensee shall include with the plan HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 48

documentation of consultation and copies of comments and recommendations on the completed plan after it has been prepared and provide to HOOPA FISHERIES, and specific descriptions of how HOOPA FISHERIES’s comments are accommodated by the plan. The Licensee shall implement the approved Project Operations Plan, which shall include the following items:

• Daily Project inflow and outflow; • Graphical plots of hourly data below the Link River (if retained in the Project

boundary), Keno and JC Boyle dams, and the JC Boyle powerhouse; • A graphical plot of hourly ramping rates; • An annual summary of non-compliance reports; • Improvements in flow monitoring at the gage stations below Project dams and JC

Boyle powerhouse; • Measurement of flows at the gage stations below the dams and JC Boyle

powerhouse; • A comparison of actual to minimum flows below each facility; • Control of river stage changes below each Project dam and JC Boyle

powerhouse; and • Seasonal Drawdown, Refill and Fluctuation Limits for Project Reservoirs

8B. Annual Project Operations Report. The Licensee shall submit an annual report with narrative and graphs summarizing the annual compilation of the project operations data to confirm compliance with minimum flows and ramp rates. The Annual Reports shall provide specific information regarding compliance with the section 10(a) license conditions, and short and long term monitoring of activities conducted pursuant to the section 10(a) license conditions. Before April 1 of each year the Licensees shall publish an Annual Project Operations Report that describes the operating history of the Project over the previous calendar year. This report shall include a general summary of the hydrologic conditions, overall project operation, and unusual events or conditions that occurred during the year. Charts shall be included which graphically show the Project’s operating parameters over the prior year, such as: inflows; outflow; days of operation at “or inflow”; and lake levels. Operating incidents that occurred during the year shall be listed and briefly described, and Final Incident Reports for these events shall be included as an appendix to the annual report. The Report shall include summaries of the data itemized in 10A. Background and Rational Compliance with Management Direction, Administrative Rules and Basin Plans: HOOPA FISHERIES’s goals and objectives for the Klamath River fish populations are to maintain and restore habitat including instream flows and natural hydrology to support healthy native aquatic species including indigenous trout, sucker, lamprey and anadromous salmonids. Habitat parameters must remain within the range that maintains the biological and requirements to support productivity, growth, reproduction, and migration of native fish. Fish survival, growth, and egg incubation and emergence


are related to quantity and quality of habitat, so if the Project impacts these parameters, fish populations and their health are affected. Huntington (2004) examined through an Indicators of Hydrologic Analysis (IHA) the degree to which the Licensee’s hydropower operations alter streamflows within specific reaches of the Klamath River. A set of 35 hydrologic parameters was examined for the JC Boyle bypass and peaking reaches. In the bypass reach, the Project reduces the magnitude and variability of monthly flows from the median by 75%. Between-year variations in minimum flows have been virtually eliminated as flow releases from JC Boyle Dam are held at very low and constant levels except for occasional high runoff that exceeds the capacity of the powerhouse and caused spill into the bypass reach. In addition, annual extreme high flows occur about 2 months earlier while low flows about 5 to 6 months earlier than compared to without Project conditions. High pulse flows have been eliminated while duration of low flow pulses has been dramatically extended. In contrast, below the powerhouse, the Project reduced median flows, and substantially increased flow variability during most months of the year, particularly for low flow conditions. The magnitudes of minimum flows were consistently and drastically reduced while maximum flows were consistently increased. Annual extreme high flows first occurred 2 to 3 months earlier while low flows were 4 to 6 months earlier. The frequency of high pulse flows increased by more than 3000% and low pulse flows by 850%. Peaking has become the dominant feature of the river’s hydrograph in this reach, nearly eliminating the monthly and seasonal patterns of natural variation in flow. All of these changes were to a “without Project” condition that is itself affected by upstream variations including irrigation projects. Huntington (2004) also analyzed the half hourly stage data from 3 different water year types of 1994, 1995, and 1999 to compare the percentage of days on which a given hourly up or down ramp was exceeded. The results of the analysis documented daily maximum up and down ramp rates at the USGS gage site below the powerhouse that ranged from zero to well over 1.2 feet per hour, with the highest rates experienced during the dry (1994) and wet (1999) years. The analysis demonstrated that the hourly ramp rate of 9 inches per hour (0.75 feet per hour) was exceeded from 30 to 38% of the time. Hydrologic modeling should also consider the importance of riparian and wetland areas that are known for their natural ecological functions of storing water during high flows and release of water during low flows, thereby moderating extreme flows in river systems. With construction of Keno, JC Boyle, Copco 1 and Iron Gate dams, much of the mainstem riparian riverine and nearby wetland system along the Klamath River was inundated. In addition, peaking flows in the JC Boyle have coarsened the bedload and much of what was once the riparian along the mainstem has become a varial zone of alternately wetted and dried river bed with little riparian function left. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 50

9. Fish and Wildlife Enhancement Plan 9A. Fish and Wildlife Habitat Enhancement Plan. Within one year of license issuance, the Licensee, in consultation with HOOPA FISHERIES and affected agencies, shall develop a Fish and Wildlife Habitat Enhancement Plan. The purpose of the Plan is to develop strategies to implement mitigation measures for ongoing impacts to fish and wildlife populations from Project facilities and operations. Implementation of the Plan will be to increase the success of anadromous fish reintroduction and potamodromous restoration and to support resource protection measures for project-related impacts not otherwise covered by specific license conditions, including projects that enhance and improve wetlands, riparian and riverine habitats, and riparian, aquatic and terrestrial species connectivity that may be affected by the continued operation of the Project. The Plan shall be developed and implemented in coordination with state and federal fish and wildlife agencies including HOOPA FISHERIES, CDFG, USFWS, and NMFS, and with the major land management agency, BLM. The Plan shall identify strategies and be funded by the Licensee to implement habitat enhancement measures in mainstem reaches and tributaries containing native fish and wildlife species. The Licensee will restore fish habitat above and below the Project to mitigate the continued effects of the Project on fish and wildlife habitat. The Licensee shall provide funding for this mitigation throughout the term of the license, though priority for Projects will be given for the first 15 years. These measures shall focus on appropriate reaches within and above the Project. In cooperation with landowners, the Plan measures shall focus on restoration of riparian areas and wetlands, instream flow and water quality restoration, and land acquisition. The Plan shall include procedures based on common methods utilized in fisheries and wildlife science, including state-of-the-art techniques, for prioritizing and selecting habitat restoration, conservation, and/or acquisition projects. The Plan should provide temporal and spatial management strategies that restore and maintain optimum habitat components for the diverse wildlife and vegetative species present within the Project. The Fisheries Passage Committee will review all fish habitat protection, mitigation, and enhancement proposals prior to approval. Mitigation for riverine salmonid habitat is proposed as follows:

A. Compensatory mitigation for a total of five miles of bypass channel (four miles below JC Boyle Dam and one mile below Copco 2 Dam).

B. Compensatory mitigation for a total of 41.7 miles of riverine channel that

has been inundated by project reservoirs (9.1 miles for Iron Gate reservoir, 4.4 miles for Copco reservoirs; 3.7 miles for JC Boyle reservoir; and 23 miles for Keno reservoir).

C. Compensatory mitigation for fish passage facilities that are less than

100% effective for upstream and downstream migrating fish. D. Habitat mitigation may include cooperatively funding with water users in

the Klamath basin, adult and juvenile fish passage facilities at irrigation diversions or other constructed fish barriers in the upper basin. Habitat


enhancement may also include purchase of instream water rights. The Licensee shall fund the planning and implementation of projects on federal lands to meet associated agency requirements under the National Environmental Policy Act and the Endangered Species Act. The Licensee shall fund the maintenance and monitoring of these projects to determine their effectiveness.

9B. Funding. The Licensee shall establish a habitat fund to accomplish the purposes of the Habitat Enhancement Program. This fund amount shall be developed in consultation with HOOPA FISHERIES and affected agencies. Commencing on the second year after license issuance, on the same date that the Annual Report is submitted pursuant to Condition 1, the Licensee shall annually deposit a designated amount, adjusted annually based on the Consumer Price Index, into the fund. The Licensee shall use these funds to conduct restoration, conservation, and/or acquisition projects as described in an Annual Work Plan developed to implement this plan. Operation and maintenance costs associated with habitat enhancement will also be covered by this fund. 9C. Vegetation and Noxious Weed Plan. Within two years of license issuance, the Licensee shall develop a vegetation management plan in consultation with resource agencies including HOOPA FISHERIES, CDFG, BLM, and USFWS. The Plan should include strategies for managing native vegetation to optimize habitat for wildlife species and control invasive weed species. The Plan should guide land management practices on company-owned lands such as management of forest, shrub and grassland communities to contain, control, and suppress exotic and invasive weeds so they do not act as a source for infestations downstream or on adjacent property or compromise the integrity of native fish and wildlife habitat. Issue and Rationale Compliance with Management Direction, Administrative Rules and Wildlife Species Plans: HOOPA FISHERIES’s goals and objectives for the Klamath basin are to maintain and restore habitat including connectivity and productivity to support healthy fish and wildlife populations. Habitat parameters must be restored to the range that maintains the biological and requirements to support productivity, growth, reproduction, and migration of native wildlife. Fish and wildlife productivity, migration corridors, dispersal, and reproductive success are directly related to quantity and quality of habitat, so if the Project impacts these parameters, wildlife populations and their health are affected. A Fish and Wildlife Habitat Enhancement Plan is necessary to mitigate for irrevocable impacts to fish and wildlife resources and their habitats caused by ongoing and continuous Project operations and facilities. This condition requires the Licensee to improve habitat quantity and quality for fish and wildlife above and below the Project commensurate with the loss of riparian, riverine, wetland, and upland habitat caused by ongoing operation of the Project.


The Project continues to reduce fish habitat quantity and quality through the continued loss of nearly 41 miles of instream fish habitat, including the fish habitats of the mainstem Klamath River and its tributaries within the Project's reservoirs. These reaches of the river were important areas for chinook, coho, steelhead, and Pacific lamprey. Even with the Licensees implementing fish passage, production capacity for redband trout, ESA-listed suckers and reintroduced anadromous species will be reduced due to the continued occupation of the river habitat by Project reservoirs. Cumulative and Continuous Impacts to Riparian, Wetland, Riverine and Botanical Resources: The Klamath Hydroelectric Project blocks access to historic anadromous fish habitat and fragments native salmonids and other native potamodromous fish species from populations below, within, and above the Project. The Project results in conversion of a free flowing mainstem river to a series of five reservoirs. Construction of the Project’s reservoirs and alteration of the Klamath River’s hydrology and geomorphology has impacted fish and wildlife through the loss or conversion of over 80 acres of riparian habitat. The operation of the JC Boyle, Copco and Iron Gate reservoirs affect up to 131 ha (324 ac) of drawdown zone that have a limited amount of wetland or riparian vegetation. Current peaking operations in the JC Boyle peaking zone also affect up to 23 ha (58 ac) in the varial zone. Flow alteration and Project operations have inundated riparian, wetland and riverine habitat, diminished remaining riverine and riparian habitats and caused ongoing entrapment and mortality of fish and wildlife species, and increased the establishment of non native species such as reed canary grass to the detriment of native riparian plant and wildlife species. The JC Boyle spillway overflow and failure of the waterway power canals results in impacts to riparian and aquatic habitats by erosion and sediment deposition. Road cast along the JC Boyle access road has also deposited road materials in the Klamath River, causing turbidity and sedimentation problems, and reducing riparian and riverine habitat quality. There are large gaps in riparian/wetland habitat, particularly along Iron Gate and Copco reservoirs, but also along JC Boyle, that limit habitat quality for amphibians, reptiles and other wildlife species and reduces connectivity. In addition, most reservoirs provided very little habitat for breeding amphibians due to frequent water level fluctuations. Western pond turtles are found throughout the Project although use is more concentrated around shorelines with basking sites in lower gradient portions of the river. Western pond turtles are affected by fluctuating shoreline reservoirs that cause reduced basking habitat and juvenile habitat. Existing basking sites should be protected and opportunities to increase basking sites should be pursued in areas identified as lacking these components. The BLM has identified potential locations where basking structures (boulders and logs) could be placed in the vicinity of suitable nesting and over winter habitat. These type structures would also have high value for other wildlife species for foraging and roosting. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 53

Aquatic furbearer species such as beaver, river otter, mink, and muskrat are impacted by lack of riparian vegetation and denning sites due to peaking impacts causing shoreline erosion and degradation of riparian vegetation. Project operations also result in the proliferation of non-native species, resulting in competition for available resources. The extirpation of anadromous species within and above the Project affected potamodromous species through the loss of marine derived nutrients and an available prey base. Non-native invasive plant species either documented in the area include but are not limited to Canada thistle, cheatgrass, common toadflax, dalmation toadflax, leafy spurge, musk thistle, scotch thistle, puncture vine, reed canarygrass, spotted knapweed, whitetop, and yellow star thistle. These species have the greatest potential for impact to native wildlife and wildlife habitat.

10. Recreation 10A. Recreation Study and Instream Flow Recommendations. HOOPA FISHERIES recommends flow recommendations for recreation for the Klamath River which reflect instream flow recommendations for fish and aquatic life (see Condition 6. Streamflow in Bypass, Peaking and Regulated Reaches). 10B. Flow Information. The Licensee shall provide hourly flow information and projected 24-hour flow information to the public via a telephone hotline information service below each Project facility. Issue and Rationale Compliance with Management Direction, Administrative Rules and Wildlife Species Plans: HOOPA FISHERIES’ mission statement embodies goals for recreation objectives: protect and restore fish and wildlife and their habitats for present and future use. Therefore, HOOPA FISHERIES statutes and policies are to further the mission to protect and restore fish and wildlife habitats so that the public may enjoy consumptive and non-consumptive uses of fish and wildlife populations. These include fishing, hunting, wildlife watching, developing personal species life lists, and more. In addition, fish management basin and wildlife species plans have objectives to provide for use and enjoyment of fish and wildlife populations by providing public opportunity and access. Therefore, these recreation objectives for the Klamath basin fish and wildlife populations directly are mandated for our statutes to maintain and restore habitat. Recreation Study Results: The angling recreation study conducted by the Licensee led to technically flawed results due to low sample sizes, misleading questions and false conclusions. The results disregard historical information that showed that the river, in the absence of the Project, was once a highly productive system with abundant trout populations known for their large-sized trout, and produced the third largest salmon runs on the Pacific west coast. HOOPA FISHERIES disagrees with HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 54

conclusions of the recreation flow analysis, in which the existing condition of low flows in different segments of the Klamath River are considered the optimum flow range for recreational angling. The flow evaluation curves incorrectly conclude that lower flows tend to provide the best quality fishing conditions since it provides better wading access, lower velocities in different habitats, and less turbulence in the rapids. The analysis of flow duration curves is based on average daily flows, which lead to misleading conclusions on impacts of flow fluctuations to angling use. The FLA generally describes optimum fishing in different reaches of the Klamath River from Link River to Copco 2 as low flow conditions with the fundamental assumption that the best condition for angling is when conditions are the most favorable for wading under existing peaking and flow fluctuation conditions. In addition, a very low number of anglers were interviewed for each reach with 17 interviewees for fishing on all upper reaches of the river above Iron Gate Dam. These ranged from 4 to 8 total anglers for each flow per reach. The interviewees were not given the choice of angling under a river with restored flow but only the existing river with ongoing peaking and ramping impacts. Abundance, size, and distribution of fish along with angler success are inextricably tied to quality, quantity and productivity of the habitat. Many of the anglers interviewed expressed valid concerns of separating out the biophysical characteristics of the river caused by Project operations from their ability to successfully fish the river. A more natural river hydrograph along with better water quality conditions and fish passage would yield more abundant native fish populations and in turn lead to higher quality of fisheries. The peaking and ramping operations along with other Project impacts such as reduced passage have reduced the productivity of the river, and in turn angler success and satisfaction over the long term. The study relies on existing hydro Project conditions that have substantially reduced trout abundance, size and distribution. For example, anglers that were interviewed for their preference of fishing conditions in the Keno, bypass and peaking reaches naturally preferred lower flows because fish are more concentrated and easier to catch in low flow conditions. However, lowered productivity has strongly affected anglers’ ability to catch fish in what was once a highly productive system known for its large and abundant trout populations (Fortune et al. 1966). Since anglers were asked to characterize optimum angling conditions given existing Project conditions, without consideration for natural flow conditions, inappropriate flow evaluation curves were drawn for acceptable and optimum fishing conditions. These curves underestimate and recommend minimum flows for fishing well below the natural flows of the river. For example, the Link River flow evaluation curve for fishing with optimum flows is 100 to 1,500 cfs with best flows at the lower end. The report states that minimum flows in the Link River bypass have been higher than 90 cfs even in the driest period and are often in the 250 cfs to 600 cfs range from May through December, and therefore concludes that the power diversion effects are beneficial because the Project generally prevents higher flows that would be caused by the HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 55

additional flow of 1,450 from the Eastside canal. The 1,450 cfs diversion is higher than the allocated take of water for the Eastside diversion and may be in violation of the certificated water right for the diversion. Additionally, HOOPA FISHERIES biologists have frequently observed flows in the bypass reach of less than 50 cfs. Public Access: Developed recreation in Oregon includes an access trail along the Westside of the Link River, a PacifiCorp park and camping facility located near Keno Dam, and BLM access sites along the JC Boyle Peaking reach. More recreational sites such as camping and boating are found at Copco and Iron Gate reservoirs. The recreation use in the Link River reach is limited and is primarily angling, with some whitewater kayaking below the powerhouse tailraces. The recreation use in the Keno and JC Boyle Bypass reaches are primarily angling with limited amounts of whitewater boating, although hunters also use the area. The recreation use in the JC Boyle Peaking Reach is dominated by commercial whitewater rafting that has effectively used the peaking flows to provide a whitewater journey down the Klamath River from the Spring Input to Copco Reservoir. Angling also occurs at some BLM access points such as the Frain Ranch and Stateline, and is more popular in the California segment where gradient is more moderate and peaking is attenuated with distance from JC Boyle Powerhouse. Impoundments created by the Project, including JC Boyle, Copco and Iron Gate, are accessible to the public and used primarily for flat water recreation such as boating, angling, waterfowl hunting, and swimming. What are use rates? A telephone hotline service should be provided to the pubic to provide current and projected 24 flow information below each Project facility.

11.Project Abandonment and Decommissioning

11A. Project Abandonment and Decommissioning. In the event that PacifiCorp proposes to abandon any of the Project facilities, the Licensee shall remove or modify Project facilities and restore pre-Project conditions in any manner reasonably required by federal and state agencies to maintain fish and wildlife production in the Project affected area. Issue and Rationale Decommissioning and Removal Evaluation: The re-licensing process is designed to determine whether an existing Project should be granted a new license. To answer that question, the Commission, the public, and policy makers must have information on the Project’s impacts and benefits as a whole, not just the changes proposed by the licensee. Due to the high public interest in this Project re-licensing, FERC will need to complete an EIS on the re-licensing of the Klamath Project based on FERC’s regulation requiring it to consider “the degree to which the effects on the human environment are likely to be highly controversial” (40 CFR 1508.27). FERC’s development of an EIS will require analysis of a full range of alternatives, including the alternatives of issuance of a HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 56

non-power license or Project retirement, for any one or more of the Project facilities. Regulation 16 U.S.C. s 808(b) states that “Non-power licenses may be issued at the motion of an interested party or on the Commission’s [FERC’s] own motion”. FERC could determine that a non-power license is necessary if it concluded that power production needs were outweighed by economic, social, recreational or environmental considerations. Therefore, the consideration of what conditions to attach to a new license and the questions involved in determining whether a non-power license is necessary requires the preparation of an EIS. The Licensee must provide the necessary information to FERC and stakeholders to make an adequate determination of public benefits and costs for continuing or decommissioning and removal of all or part of the project. The California Energy Commission (2003) conducted an energy analysis with a perspective of a high level analysis. The CEC concluded that while the Licensee will be operating with a deficit of power generation to use in the next decade, the relative contribution of the Klamath hydro Project was considered nominal, and in fact close to a “statistical error” in the entire power production of the Licensee’s facilities. The CEC identified decommissioning as a viable alternative that should be examined during the FERC re-licensing proceedings. Dam Decommissioning and Removal: Hydropower generation may decline as an energy source in the future. In 30 years, resource economics and environmental impacts as well as alternative sources of energy development may make some hydroelectric facilities obsolete. HOOPA FISHERIES believes it is in the public interest and makes prudent business sense for FERC to require the operator to establish a dam decommissioning and removal provision for the project. However, it is recognized that Project abandonment and decommissioning costs may be very expensive.

12. Project Inspections and Access

12A. Project Inspections and Access. The Licensee shall allow state and federal regulatory agencies, including HOOPA FISHERIES, access to, through, and across Project lands and works for inspecting fishway facilities and records, including monitoring data, to monitor compliance with this license. The Licensee shall allow such inspections upon the entity requesting the inspection providing the Licensees with reasonable notice of such inspections and agreeing to follow the Licensee’s standard safety and security procedures when engaged in such inspections. Issue and Rationale Inspections of Project fishway facilities and data records and summaries are needed to provide an opportunity for the regulatory agencies to determine compliance with environmental license conditions adopted in the license and to track development and implementation of resource plans. Under the existing license, there is little to no tracking of impacts of Project fishway facilities and operations to natural resources. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 57

FERC environmental inspections occur at best annually. When HOOPA FISHERIES staff conducted research at the JC Boyle Dam facilities, flows in the ladder ranged from non-existent to raging white water, indicating non compliance with existing license conditions. The relicensing process has strongly illuminated the need to provide regular and frequent inspections of facilities and operations and to make access available to regulatory personnel for environmental license conditions.

13. Water Quality in Bypass, Peaking and Regulated Reaches 13A. Water Quality Monitoring Plan. The Hoopa Valley Tribe regulates water quality on the Klamath River portion of Reservation waters pursuant to 33 U.S.C. § 1377. The Licensee shall implement mitigation measures and conduct water quality monitoring pursuant to the Water Quality Management and Monitoring Plan Approved by the Hoopa Valley Tribe, ODEQ and CSWRCB in connection with Clean Water Act § 401 water quality certifications issued by those agencies. 13B. Failure to Meet Water Quality Certification. To the extent that it is infeasible to meet water quality objectives set forth below or in water quality certifications by ODEQ or CSWRCB through modification of Project facilities and operations, the Licensee shall prepare a decommissioning amendment for the subject facility in consultation with state, federal and tribal stakeholders in order to achieve compliance. Issue and Rationale In this section, the following water quality parameters are addressed in order: - Water temperature - Nutrients - Periphyton and aquatic macrophytes - Dissolved oxygen, - pH - Ammonia toxicity - Cyanobacteria and cyanobacterial toxins - Taste and odor compounds - Fish parasites For each parameter, we provide background information, as necessary; we present information about the parameter’s existing condition in the Klamath River; we discuss how the KHP contributes to the present condition of that parameter; and then we recommend the means by which the parameter’s adverse effect on the river’s water quality can be remedied. Before providing detailed information regarding specific water quality parameters and the KHP’s effects on them, a few words regarding PacifiCorp’s water quality modeling are required. PacifiCorp (2005d) presents the results of modeling calibration and verification. Examination of the figures in the appendix shows that the model predicts flow and temperature quite well, but does not accurately predict dissolved oxygen, HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 58

nutrients, or algae. It is important to keep the differences in accuracy between the various parameters in mind when evaluating model results. Flow and temperature are based on the laws of physics, and modeling them is a long-established practice. Dissolved oxygen, nutrients, and algae are subject not only to the laws of physics, but also to chemistry, biology, and ecology, which are far more complex, unpredictable, and difficult to represent mathematically. To compound the problem, compared to flow and temperature, far less data is available for these parameters to calibrate and verify the model. TEMPERATURE Existing conditions in Klamath River The Klamath River is recognized as impaired with regard to water temperature by the North Coast Regional Water Quality Control Board temperature-impaired (NCRWQCB 2001). Kier Associates (1999) noted acutely stressful water temperature conditions on the mainstem Klamath River and the potential for temperature stress to contribute to juvenile salmonid disease epidemics. Data show that water temperatures in the mainstem Klamath River consistently exceed stressful for steelhead in all years (Figure 1) and sometimes exceed lethal conditions for juveniles of Pacific salmon species such coho and chinook (Sullivan et al., 2000). The locations displayed are in the Middle Klamath reach from near Happy Camp to just above Weitchpec. The floating weekly average water temperature is calculated by averaging the average daily water temperature for sampling day and the three days on either side of each day. The highest value floating weekly average for an entire year is the maximum floating weekly average or MWAT (Welsh et al. 2001). Although the MWAT can be used as an index for duration of stress to which fish are exposed, it masks extreme highs that would be reflected in a floating weekly maximum temperature (MWMT). Figure 2 shows the MWMT at mainstem Klamath River locations between Iron Gate and Weitchpec with acute temperature problems extending from just above the Shasta River to Weitchpec, where the Trinity River joins the Klamath River and moderates its temperature.


Figure 1. Maximum floating weekly average temperatures (MWAT) of the Klamath River for nine locations for the years 1997-2002. Data from KRIS Version 3.0 (TCRCD 2004). DS = downstream, US = Upstream.


Figure 2. This chart shows an increase in floating weekly maximum from April through August at six Klamath River locations in 2000 with only R-Ranch below Iron Gate attaining a maximum of below 25° C. Data from KRIS V 3.0 (TCRCD 2004). An MWAT of 25° C indicates that maximum daily temperature exceeded lethal for levels for steelhead (26.5° C) as characterized by Sullivan et al. (2000). For example, Figure 3 shows the minimum, maximum and average temperature of the Klamath River at Seiad Valley in 2002. While the MWAT was 25.39° C, the peak maximum reached 27.14° C. McCullough (1999) recognized that all salmonids ceased growth and were under stress above 20° C. Figure 4 shows temperatures of the Klamath River above the Salmon River exceeded 20° C in 1996 for weeks at a time in July and August. Salmonids would have no period during the night to recover from temperature stress, if they were not able to find cold water refugia at the mouths of tributaries. The above data clearly illustrate that mainstem Klamath River water temperature alone is a sufficient stressor to cause increased susceptibility of disease and even direct mortality of salmonids in many years. Temperature acts in concert with other stressors in affecting fish health and has synergistic effects on other water quality parameters such as pH, D.O. and ammonia.

Figure 3. The minimum, average and maximum chart for the Klamath at Seiad Valley in 2002 shows that while the MWAT would be 25° C the max-max was over 27 ° C. Data from KRIS V 3.0 (TCRCD, 2004).


Figure 4. This chart shows that in July and August of 1996 that the Klamath River water temperature above the Salmon River rarely dropped below 20° C, which is recognized as a temperature stressful to all salmonids (McCullough, 1999). KRIS V 3.0 (TCRCD 2004). Dr. John Bartholow (2005) of the U.S. Geologic Survey has studied the mainstem Klamath for over a decade and analyzed all available data, both recent and historic. Data suggest a long-term trend towards warming with adverse implications for salmonid survival:

“The season of high temperatures that are potentially stressful to salmonids has lengthened by about 1 month over the period studied, and the average length of main-stem river with cool summer temperatures has declined by about 8.2 km/decade. Water temperature trends seem unrelated to any change in main-stem water availability but are consistent with measured basinwide air temperature increases. Main-stem warming may be related to the cyclic Pacific Decadal Oscillation, but if this trend continues it might jeopardize the recovery of anadromous salmonids in the Klamath River basin.”

Water temperatures are likely to increase due to climate change. Rising atmospheric concentrations of carbon dioxide and other greenhouse gases could lead to an increase in global mean temperatures (NRC 2004). The National Research Council report (NRC 2004) provides a description of what may occur:

HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006

“A detailed model of the Klamath basin region at 25 mi resolution has been developed by Snyder et al. (2002). Use of the model demonstrates three important kinds of changes in the hydrology of the Klamath

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watershed that could occur over the next century: (1) warming, especially at high elevations in spring (April, May); (2) higher total precipitation, especially in spring; and (3) an increase in the ratio of rainfall to snowfall and large decreases in spring snowpack. The changes modeled by Snyder et al. (2002) have strong implications for management of water resources and all aquatic species, but especially salmonids (NAST 2001, O’Neal 2002). For salmonids, the most important potential changes include altered timing of snowmelt, lower base flows, and additional warming of water in summer.”

Given that high water temperatures are widely recognized as a problem for anadromous fish in the Klamath River, global climate change has the potential to cause additional decline in the basin’s fish stocks and should be part of the context within which the KHP is evaluated in the EIS. Project Effects It is widely recognized that the KHP alters water temperatures in the Klamath River (PacifiCorp 2004). Due to the thermal mass of Iron Gate and Copco reservoirs, water temperatures in the mainstem Klamath below Iron Gate Dam are cooler in spring, and warmer in late summer and fall, than would exist if the KHP were absent (PacifiCorp 2004, PacifiCorp 2005, Deas 2004). The KHP decreases water temperature in the spring and early summer by at least 5° C and also increases stream temperatures in late summer and autumn by at least 5° C (Figure 5). Due to variations in weather, the timing and magnitude of these temperature deviations will vary from year to year. The EPA Region 10 Guidance for Pacific Northwest State and Tribal Temperature Water Quality Standards (U.S. EPA 2003) recommends temperature limits for various life history stages for the protection of Pacific salmon species. For spawning, U.S. EPA recommends that the maximum seven-day floating average (7DADM) not exceed 13° C, which is shown on Figure 5 as a reference line. Historic spawning in the reach below Copco Dam began in mid-October (Snyder 1931) and chinook salmon spawning takes place today from Iron Gate Reservoir to Happy Camp during that period (Figure 6) (Catalano et al. 1996, Magnusen et al. 2001). Model outputs in Figure 5 show that the Klamath River water temperature without the KHP would begin to fall to lower than 13° C for at least brief periods, as early the first week in September. Natural temperatures would consistently meet U.S. EPA thresholds (13 C 7DADM) three weeks earlier than temperature of flows emanating from Iron Gate Dam. Eggs laid in the Klamath River below Iron Gate at higher than optimal conditions are likely to have higher pre-hatch mortality, a greater rate of developmental abnormalities, and lower weight as alevins (McCullough 1999).


Figure 5. PacifiCorp water quality modeling output showing water temperatures at Iron Gate Dam for the year 2000, comparing existing condition (with project) and without project scenarios (PacifiCorp 2005c). References for salmonid spawning and the lower limit for salmonid growth are from U.S. EPA (2003). Although the viability of eggs and fecundity of female chinook salmon have not been measured in the wild, Iron Gate Hatchery does track the fecundity of hatchery fish. Figure 7 shows that fertility of eggs dropped as low as 66% in lots of fish spawned in early October, when temperature stress related to elevated water temperature from Iron Gate Reservoir is occurring. As temperatures drop, fertility increased to a maximum of 96% by November 7. As water flows downstream from Iron Gate, the thermal lag becomes less pronounced, but is still visible at Seiad Valley (river mile 128.5), 60 miles downstream of Iron Gate Dam, increasing temperatures between 2˚ C to 5˚ C for most of October and November (Figure 8). The Klamath River without the Klamath Hydroelectric project (WOP) alternative would attain fall to temperatures suitable for chinook salmon spawning weeks before current existing conditions (EC), similar to just below Iron Gate Reservoir. Since this reach is heavily used by fall chinook salmon for spawning, detrimental effects on fecundity, fertility and egg survival are likely to occur here as well.


Figure 6. Chinook salmon spawning surveys below Iron Gate Dam (Reach 1) downstream to Happy Camp (Reach 6) show that spawning begins in mid-October in the entire reach. Data from USFWS (Catalano 1996).

Figure 7. Iron Gate Hatchery female fall chinook salmon is indicated by the percent of fertile eggs present in spawning lots on various days from early October to early November. Data from California Department of Fish and Game Region 1. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 65

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Figure 8. Results from PacifiCorp’s water quality model comparing water temperatures in the Klamath River at Seiad Valley in the year 2000 under four different scenarios. WOP = without project (all dams but Link removed), WO IG-COP = existing condition with Iron Gate and Copco removed, EC = existing condition, WO IG = existing condition with Iron Gate removed. Figure from Deas (2004). Since the construction of Iron Gate dam, there has been a shift in the timing of the fall Chinook spawning run that is arguably due to the KHP’s impact on river temperatures (Michael Belchik, personal communication). The compression of the run timing of fall Chinook not only makes fish more vulnerable to harvest but can cause higher densities in the stream as they join later-running Trinity River fish in the lower Klamath River. High concentrations of salmon in combination with high water temperatures are thought to have contributed to the September 2002 Klamath River fish kill (CDFG 2003 and Guillen 2003). The U.S. EPA (2003) and McCullough (1999) both recognize 4° C as the lower temperature lower limit for salmonid growth. While Klamath River flows would naturally drop below 4° C in December and January, they would occasionally rise above that level during that period whereas reservoir outlet flows stay consistently below it. Also, with project flows remain under 4° C early December to late March, where without project temperatures would exceed that threshold consistently starting in February (Figure 5). Warm incubation temperatures accelerate time of emergence. Therefore, it is likely that Klamath River fall chinook fry emerge from the gravel earlier than they would if incubation temperatures were optimal throughout their gestation. Early emerging fry then have to withstand sub-optimal stream temperatures because of KHP-depressed stream temperatures through late March. Small chinook salmon juveniles in the Klamath River migrate downstream slowly (PFMC 1994). Increased residence time in the mainstem exposes fish to prolonged stress, increasing their likelihood of becoming infected with parasites (see Fish Disease section below). In addition, the larger a smolt


is before entering the ocean, the higher its chances of surviving to maturity and returning to spawn (Nicholas and Hankin 1988). The early summer cooling may provide some benefit to juvenile fish, but the period is short (less than one month total in the year 2000), and the magnitude is small. Due to the short duration and magnitude of this beneficial cooling, the benefits are likely to be far outweighed by the detrimental effects to late summer, spring, and fall temperatures. Modeling from the year 2000 (Figure 5) (PacifiCorp 2005c) shows that the project had: beneficial cooling of 0-5˚C for the last 10 days of May, detrimental heating of 0-4˚C for the first half of June, beneficial cooling of 3˚C for two weeks in late June, detrimental heating of approximately 4˚C in the first 7 days in July, no difference for most of July, a cooling benefit of approximately 2˚C for approximately 5 days in late July/early August, and then detrimental heating beginning in August and lasting through the end of fall. In the J.C. Boyle Bypass Reach, located between Copco and Keno Reservoirs, there are springs that contribute approximately 225 cubic feet per second of clean, cool water. These springs could be among the most significant thermal refugia on the entire mainstem of the Klamath River and there is evidence they were supporting summer holding by spring-run chinook prior to the construction of Iron Gate Dam. Spring-run chinook were historically the most abundant salmonid species in the Klamath Basin, but declined because of blockage of migration and deterioration of habitat (NRC 2004). The U.S. EPA (2003) points out that access to refugia is essential for river systems where attainment of optimal mainstem temperatures is not possible. The critical role of thermal refugia in maintaining the viability of anadromous salmonids in the Klamath Basin has become increasingly clear in recent years (Belchik 1997, McIntosh and Li 1998, Watershed Sciences 2002). Remediation In response to FERC’s AR-1 request, PacifiCorp used its water quality model to analyze various possible ways to reduce the KHP’s effects on temperature. PacifiCorp (Scott 2005) summarized its findings as follows:

“The results of the analyses indicate that potential reservoir water temperature management using selective withdrawals, curtains, or flow augmentation offers only modest, if any, improvements to water temperatures in the Klamath River downstream of Iron Gate dam. Furthermore, the alternatives examined do not provide appreciable differences in regard to their relative effect on fish.”

FERC then requested PacifiCorp to complete additional modeling regarding selective withdrawal options. PacifiCorp (2005b) subsequent investigations showed that the measures would be ineffective in mitigating project impacts:

Based on these results, PacifiCorp concludes that the additional revised selective withdrawal scenarios do not provide effective control of


temperatures below Iron Gate dam, and therefore do not merit more detailed design evaluation under Part (b) of this AIR.

Even if the alternatives PacifiCorp investigated could reduce water temperature, it would not be a good idea because it would likely lead to increased nutrients being released downstream. Regarding Copco reservoir, PacifiCorp (2005a) stated:

“Consideration was given to turning the lake over earlier through implementing selective withdrawal earlier in the season. However, concerns over mixing nutrient rich bottom waters into the photic zone and possibly creating beneficial conditions for primary production was deemed undesirable.”

Even if water temperatures could be altered for spawning or rearing periods, only dam removal would provide access to important thermal refugia. PacifiCorp’s own analyses make it clear that the KHP’s effects on water temperature are immitigable; therefore, the only way to substantially reduce the impacts is to remove all KHP dams and drain the reservoirs. NUTRIENTS Background information Nutrients do not directly affect salmonids, but impact them by stimulating the growth of algae and aquatic macrophytes to nuisance levels that can adversely impact dissolved oxygen and pH levels in streams. U.S. EPA (2000) and Tetra Tech (2004) provide excellent summaries of the literature on the subject. Existing conditions in the Klamath River The quality of water coming out of Upper Klamath Lake in the summer is extremely poor and often full of live and/or dead algae. Nutrient concentrations generally decline as the Klamath River flows downstream. There are three reasons for this: 1. Dilution by springs and clean tributaries 2. Periphyton growing on the bed of the river removes nutrients from the water column 3. Denitrification by microorganisms in the hyporheic zone below the river converts nitrate into inert atmospheric nitrogen 1. Dilution Even if the river did not have the capacity to assimilate nutrients, nutrient concentration would still decline as the river flows downstream from Keno to Iron Gate due solely to dilution of low-quality Klamath River water with high-quality water from tributary and spring flow inputs. These inputs include springs in the J.C. Boyle bypass reach (225 cfs) and tributaries between Link River dam and Iron Gate dam. The tributaries are Spencer Creek (approximately 20 to 200 cfs), Shovel Creek (10 to 100 cfs), Fall Creek (30 to 100 cfs) and Jenny Creek (30 to 500 cfs). Spencer, Shovel, and Jenny creeks all have irrigation diversions, so the actual quantity of water entering the Project may be


less than stated here (PacifiCorp, 2004). The sum of these inputs ranges from 315 to 1125 cfs. As demonstrated in a comparison of flow at USGS gages from Iron Gate Dam down to Turwar near the mouth of the river (Figure 9), the river picks up many substantial tributaries on its path to the ocean. With the exception of the Shasta, and perhaps the Scott, nearly all these tributaries are cleaner and cooler than the mainstem Klamath, greatly increasing the likelihood of improved water quality. 2. Assimilative Capacity of Periphyton Benthic algae, also know as periphyton or attached algae, can take nutrients dissolved in water and assimilate them into their cells as they grow. This can enhance water quality by removing nutrients from the water, but it can also release nutrients when the algae decompose, causing diurnal D.O. and pH swings by photosynthesis/respiration cycles. 3. Denitrification in River Reaches Denitrification is a process in which certain organisms can convert nitrate (NO3) to atmospheric nitrogen (N2). The result is enhanced water quality, due to the reduction in productivity that occurs because a form of nitrogen readily available to organisms (nitrate) is converted into a stable form of nitrogen that is essentially unusable by most organisms (atmospheric nitrogen). Denitrification is known to occur in the hyporheic zones of rivers and streams (Sjodin et al., 1997 and Holmes, 1996). The hyporheic zone is the area of water-saturated sediment beneath and beside streams where ground water and surface water mix (Edwards, 1998). Denitrification most often occurs with the following conditions: low hydraulic conductivity, long flow path, reduced oxygen supply, adequate nitrate supply, and adequate supply of labile organic carbon (Edwards, 1998). The amount of nitrogen removed from some rivers due to denitrification can be extraordinary, especially those with a high rate of interchange between surface water and gravel alluvium. In Colorado’s South Platte River, denitrification rates varied between 2 and 100 mg of nitrogen per square meter per hour. During mid-summer, a 90% reduction of nitrate was achieved in a 6 km long reach. On an annual basis, close to half the nitrate input to a 100-km reach was removed by denitrification (Sjodin et al., 1997). It is unknown how much denitrification is currently occurring in the Klamath River, or how that amount compares with the amount of nitrogen assimilated by periphyton.


Figure 9. A comparison of discharge at USGS gages from Iron Gate Dam down to Turwar in summer and early fall of 2004. Adapted from NCRWQCB et al. (2005). Figure 10 shows a typical example of the longitudinal gradient in nitrogen concentrations in the peak of the summer months. Only inorganic forms of nitrogen (nitrate and ammonia) are immediately available to fuel growth of periphyton and aquatic plants, organic nitrogen must first decay into ammonia before it can be utilized. Organic nitrogen is the most common form of nitrogen across the Klamath River. High levels of inorganic nitrogen are present throughout the upper reaches of the Klamath River. Beginning at the outlet of Iron Gate Dam (river mile 189.73), dense mats of periphyton and aquatic plants cover the river bed during summer. They are extremely efficient at removing nutrients, and within approximately 40 miles, above the Scott River at river mile 146.12, most inorganic nitrogen has been removed from the water column.


Nitrogen at Klamath River Sites August 2002

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Figure 11. Longitudinal profile of mean summer (June 1 – August 31) total nitrogen concentrations in Klamath River mainstem sites for the year 2000-2004 (reservoirs excluded). Sites with less than three measurements in a summer were excluded from this graph. Figure is from Kier Associates 2005). (

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Figure 12. Longitudinal profile of mean summer (June 1 – August 31) total phosphorus concentrations in Klamath River mainstem sites for the year 2000-2004 (reservoirs excluded). Sites with less than three measurements in a summer were excluded from this graph. Figure is from Kier Associates (2005). Project effects The effect of the KHP on nutrient dynamics in the Klamath River between Iron Gate Dam and the estuary are not completely understood because of insufficient data collection and analysis; however, recent and previous studies do provide useful information. PacifiCorp (2004) cited the fact that water exiting the KHP is higher quality that water entering the KHP in support of its argument that the project benefits water quality. To understand the impacts of the KHP on water quality, the question is not “Is current water quality outflow from the Project better than current water quality upstream?” but “How does water quality in the Project area and downstream of the Project area compare to what the water quality would be in those same areas without the KHP?” Just because water quality exiting the KHP is better than KHP inflow does not mean that the Project has a beneficial impact on water quality. Project operations could very well be delaying water quality recovery. As described above, the water quality in the Klamath River should improve naturally as it flows downstream, due to freshwater inflows and the capacity of the system to assimilate nutrients. The rate at which that assimilation occurs may be altered by the Project.


To understand how the KHP affects nutrient dynamics, it is necessary to understand the nutrient dynamics of the reservoirs, free-flowing river reaches, the peaking reach, and bypass reaches. Only after these individual components are understood is an adequate understanding of the KHP’s effects on nutrient dynamics possible. The following questions need to be answered: 1. At what times of year are Iron Gate and Copco Reservoirs sources and sinks of nutrients and what is the magnitude of those sources and sinks? Kann and Asarian (2005) provided the first attempt to answer that question, and an in-progress SWRCB study (Kanz 2005) will use similar methods but with data of better spatial resolution, temporal resolution, and duration. Our best current understanding is that the reservoirs are likely sinks in April-May (Kann and Asarian 2005) and a mix of sources and sinks in June-September (Kann and Asarian 2005). Data from the fall are relatively scarce, especially during and after turnover, but it is likely that the reservoirs are sources during this season. There has been almost no data collection and analysis in the winter months, so that season remains an unknown. PacifiCorp’s (2004) Final License Application presented limited analysis of water quality data; however, some important details were obscured by averaging data over broad spatial and temporal scales. They postulated that retention of organic matter and nutrients in the reservoirs results in a net decrease in organic matter and nutrients that would otherwise continue downstream (PacifiCorp 2004). Kann and Asarian (2005) used water quality data collected by PacifiCorp and the U.S. Fish and Wildlife Service to calculate nutrient budgets for Copco and Iron Gate Reservoirs. The report concludes:

“These preliminary analyses indicate that for the Copco/Iron Gate Reservoir system, the April-November period is characterized by periods of positive and negative retention for both phosphorus and nitrogen (net positive values denote a sink and net negative values denote a source). Despite acting as net sinks for P and N over the entire Apr-Nov period, both Copco and Iron Gate Reservoirs can act as a nutrient source during critical periods (e.g., June through September), making nutrients available at such periods for downstream growth of algae and macrophytes. The more robust seasonal analysis presented here does not support an earlier PacifiCorp (2004; 2005d) broad postulation that the reservoirs benefit water quality by processing organic matter and nutrients from upstream sources. With the given data set, there is a clear indication that the reservoirs periodically increase nutrient loading downstream. Likely pathways for this increased load include internal sediment loading and nitrogen fixation by cyanobacteria.

Limitations in the spatial and temporal resolution and duration of the data make the conclusions of this study preliminary, though it is the most complete analysis thus far. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 73

The California State Water Resources Control Board (SWRCB) recently received a Clean Water Act Section 104(b) grant from the U.S. Environmental Protection Agency Region IX to conduct a nutrient cycling study on Iron Gate and Copco Reservoirs (Kanz 2005). Once collected, the data will be used to construct a detailed nutrient budget for each reservoir. Because nutrient data will be collected more frequently (every two weeks rather than monthly) and will encompass an entire year (rather than March to November), as well as include additional spatial coverage and algal sampling, the 2005 study is expected to be an improvement over the analysis of existing data conducted by Kann and Asarian (2005). The study is expected to provide information on important reservoir processes that have not yet been fully evaluated, including seasonal patterns of nutrient flux and the potential for nitrogen fixation by blue-green algae. Sampling began in May 2005 and will continue through May 2006, with results available soon after. 2. At what times of year are free-flowing river reaches of the Klamath River sources and sinks of nutrients, and what is the magnitude of those sources and sinks? As described earlier, benthic algae, also know as periphyton or attached algae, can take up nutrients dissolved in water and assimilate them into their cells as they grow. In addition, denitrification by microorganisms in the hyporheic zone of free-flowing rivers can reduce nitrogen concentrations in streams. These two processes can enhance water quality by removing nutrients from the water. The assimilative capacity of Klamath River periphyton to remove nutrients from water should be quantified. Kier Associates and Aquatic Ecosystem Sciences are currently performing data analyses for the Yurok Tribe that should provide some answers to these questions, though the analyses will be limited by the quality and resolution of the source data from PacifiCorp and U.S. Fish and Wildlife Service. Nutrient data described above and shown in Figure 10 shows that the free-flowing river below Iron Gate Dam is particularly effective at removing inorganic forms of nitrogen (ammonia and nitrate). The algal assimilation and denitrification most likely responsible for this reduction in inorganic nitrogen levels are temperature-dependent processes (Sjodin 1997), so are likely most effective in during July and August, the warmest months of the year. 3. How do bypass and hydropower peaking operations affect nutrient dynamics in the J.C. Boyle Bypass and Peaking reach? Power peaking operations in the reach below J.C. Boyle have reduced the amount of benthic algae in the KHP area (PacifiCorp 2004). PacifiCorp’s Final License Application (2004) acknowledged that power peaking operations have impacts on fish populations in the peaking reach; however they did not acknowledge that peaking operations may also have impacts on local and downstream water quality caused by reducing the assimilative capacity of benthic algae. Interestingly, PacifiCorp (2005d) does mention the diminished assimilative capacity in the peaking reach. There are three reasons for the decrease of benthic algae in the KHP flow-peaking area: HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 74

• diurnal desiccation of near-shore areas • reduced light penetration during peak flows • high velocities and associated scour

During peaking operations, flows in the J.C. Boyle peaking reach are ramped daily from a 325 cfs base flow to a 1500 cfs flow (one turbine) or a 3000 cfs flow (two turbines). The result is that the edges of the river alternate between wet and dry, substantially decreasing algal biomass at the edges of the channel. According to PacifiCorp (2004), peaking operations reduce the area of wetted streambed in the J.C. Boyle peaking reach by about 10 to 25 percent, because of the “varial zone” at the edge that is wetted and dried on a daily cycle. This reduction in wetted width likely diminishes the capacity of the peaking reach to assimilate nutrients. Peaking flows occur at times of peak electrical demand, which in the summer is typically weekday afternoons and early evenings (PacifiCorp 2004). During peak flows, water depths are greater than they would be were J.C. Boyle operating as a run-of-the-river facility. This, along with possible increases in turbidity, can decrease the amount of light available to benthic algae during photosynthetic hours. This would lead to less algal growth, less algal biomass, and less nutrient removal. High flows (1500-3000 cfs) during peaking may also scour benthic algae from the substrate and prevent their establishment and growth. Just as peaking affects periphyton, hence, water quality, so do bypass operations. The low flows in the J.C. Boyle bypass reach result in a narrow channel width. The flows in the bypass reach between Iron Gate and Copco are even lower, though this reach is much shorter in length. This affects the amount of periphyton that can grow in the channel bottom, which affects the amount of nutrients that the periphyton can remove from the water column, which affects downstream water quality. Benthic algae are included in PacifiCorp’s water quality model, but the model is not calibrated and verified for nutrients, so the effects of algae cannot be reliably determined from the model (Wells et al. 2004). Additionally, the model does not take into account factors such as scour and desiccation on the ability of algae to grow. Remediation Algaecides such as copper-based compounds could potentially be applied to reduce algae growth in reservoirs (Pascual and Tedesco 2003); however, we cannot recommend this approach due to potential for unintended downstream consequences. Copper is a heavy metal that can be toxic in sufficient concentrations, and does not degrade in the environment. Furthermore, groundwater at the Resighini Rancheria just above the Klamath estuary is contaminated with copper from an unknown source (Phil Smith, pers. comm.) so it seems unwise to risk exacerbating the situation. Dam removal would reverse KHP effects on nutrient dynamics. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 75

PERIPHYTON AND AQUATIC MACROPHYTES Background information EPA (2000) presents an excellent review of literature on how periphyton grows in response to nutrient availability, and how they in turn affect dissolved oxygen and pH. Based on that review, EPA (2000) provides a general guideline that the level at which periphyton typically starts to become a nuisance to water quality and aesthetics is 150 mg/m2. Additionally, Horner et al. (1983) conducted a literature review of 19 case studies and concluded that biomass levels greater than 150 mg/m2 often occurred with enrichment and when filamentous forms were more prevalent. Existing conditions in the Klamath River In 2004, there was a collaborative study of Klamath River periphyton by the North Coast Regional Water Quality Control Board, the Yurok Tribe, and PacifiCorp. They collected periphyton samples in the Klamath River at sites between Iron Gate Dam and Weitchpec, including tributary streams. Although this dataset spans only one algal growing season, and hence is temporally limited, it is the best data currently in existence. All parties used similar sampling methodologies (Eilers 2005, NCRWQCB et al. 2005) and the same laboratory. Additional information on this study’s results is contained in Kier Associates (2005). The 2004 periphyton data samples show interesting spatial and temporal patterns, and indicate that maximum annual periphyton levels at many sites on the Klamath River far exceed the EPA’s general guidance of 150 mg/m2 (Figure 13). In early July 2004, all sites sampled had chlorophyll a values of 82 mg/m2 or less, except for the Klamath River above the Scott River (river mile 142.61), which was 353 mg/m2. For the August samples, periphyton biomass increased at most sites, exceeding 150 mg/m2 at 5 of 9 sites sampled with the highest biomass of 706 mg/m2 at river mile 183.28 (Klamath River above Cottonwood Creek). In late August, the flow released from Iron Gate Dam increased from 615 cfs to a peak of 1320 cfs, before declining to 913 cfs. The flow increase likely caused significant scour of periphyton because biomass decreased from 706 mg/m2 at river mile 183.28 in August to 9 mg/m2 at river mile 179.23 on September 1, and biomass also declined substantially at river mile 142.61. Biomass held stable at river mile 98.5, and increased in the lower river at river miles 70.30 and 43.50. Biomass may not have declined in the lower river because the Klamath River’s channel generally widens as it flows downstream, and so the flow likely had less scouring affect and algae continued to grow. It is difficult to generalize from one year of data, and it is unknown if similar patterns occur in other years. The most common species identified in 2004 samples were Cymbella affinis (CMAF), Cocconeis placentula (COPC), Diatoma vulgare (DTVL), Epithemia sorex (EPSX), Navicula cryptocephala veneta (NVCV), and Nitzschia frustulum (NZFR). All six of these species are classified by the US Geological Survey as eutrophic and alkalophilic (NCRWQCB et al. 2005).


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Figure 13. Periphyton biomass as mg/m2 chlorophyll a in the mainstem Klamath River for the year 2004 grouped by sampling period and sorted by river mile. Sampling periods begin with year, followed by month-day range (i.e. 04 9/01-9/02 is 9/01/2004-9/02/2004). EPA (2000) general guidance of 150 mg/m2 is shown as a horizontal line on the charts.

Little or no data have been collected on aquatic macrophytes in the Klamath River. Below the Scott River, macrophytes are present only in quiet backwater areas (PacifiCorp, 2005d). They are known to be common in the Klamath River between the Iron Gate Dam and the Scott River, likely due to the stable nature of the channel in that reach (PacifiCorp, 2005d). In that reach, they may play an important role in dissolved oxygen and pH dynamics. Project effects Biggs (2000) provides a comprehensive guide to periphyton ecology and management. The review includes a summary of the three main ways in which dams affect periphyton in rivers:


“First, the placing of a dam or some form of barrage across the river alters (or completely stops) the flow of bed sediments moving down the river. This then usually enhances bed armouring (i.e., paved with very stable, large cobbles and boulders on the surface layers) which provides excellent substrata for periphyton to attain a high biomass. Second, most of the small- and medium-sized floods are prevented from flowing down the river (unless the reservoir is at storage capacity), which means that the normal flow variability is reduced and the natural ability of the system to remove excess accumulations of biomass is also reduced. Third, the reduction in flow usually also results in a reduction in water velocities, which then allows a higher biomass of filamentous green algae to develop if nutrient levels are sufficient.”

Biggs’ (2000) first and second points are likely occurring in the Klamath River as a result of the KHP. In addition, the third point is likely occurring in the Klamath River as well, but more likely because of upstream agriculture rather than the KHP. Geomorphic changes As noted in the citation from Biggs (2000) above, dam construction typically halts the downstream transport of gravel, resulting in more course substrates. The KHP has had this effect on the Klamath River below Iron Gate Dam. Larger substrates like cobble and boulder require higher flows to scour them than smaller substrates like gravel and sand. This provides a more stable substrate, increasing the amount of periphyton and aquatic macrophytes than can grow. The effect of the KHP on bed substrate likely diminishes with increasing distance downstream of Iron Gate as each successive tributary introduces gravels to replenish a portion of the deficit. Hydrologic changes Though not designed for flood-control, Iron Gate and Copco Reservoirs do influence the hydrologic regime by reducing peak streamflows during moderate and small storm events. Peak flows from tributaries such as Jenny, Spencer, and Shovel Creeks can be captured by the reservoirs. Hydroelectricity can only be generated when water flows through the turbines, not the spillways, so it is in PacifiCorp’s best interests to minimize use of the spillways. Hence, PacifiCorp may draw down its reservoirs in anticipation of storms to capture storm flows. This helps provide a stable flow regime that allows periphyton and macrophytes to flourish. Periphyton and macrophytes are sensitive to scouring in high flows so a reduction in frequency and intensity of peak flows may cause an increase in periphyton and macrophyte growth. Photosynthesis and respiration of periphyton and macrophytes is a major driver of pH and dissolved oxygen dynamics in the Klamath River so allowing an increase in periphyton and macrophytes may further degrade water quality.


While these hydrologic effects likely contribute to periphyton macrophyte growth between Iron Gate Dam and the Scott River, effects are likely insignificant below the Scott because winter storms are unregulated in the Scott and it contributes large amounts of water during storm events. Nutrients Many factors govern the biomass of periphyton that occurs in a stream at any given time. The explanations here are abbreviated; for full details see Biggs (2000). The most important include the amount of available nutrients, light, temperature, and number of days since scour (Biggs 2000). When nutrients and light are adequate to fully meet the demands of the periphyton community, then temperature governs the rate of accrual. The upper limit of biomass accrual is then determined by nutrient concentration and grazing intensity. Present-day (with KHP) nutrient concentrations in the Klamath River below Iron Gate Dam are likely higher than they would be without the KHP. The reasons for this are discussed above and include nitrogen fixation in KHP reservoirs, reduction in assimilative capacity through peaking operations; bypass operations, and inundation of free-flowing river reaches by reservoirs. This increase in nutrients likely leads to an increase in the amount of periphyton and aquatic macrophytes, which degrades pH and dissolved oxygen conditions, harming fisheries. Remediation The coarsening of the streambed below Iron Gate Dam could potentially be remedied by gravel augmentation, though the quantity of gravel required to fully compensate for KHP effects would likely be prohibitively expensive, and could cause damage to the stream where the gravel was removed. Dam removal would allow gravel to move downstream at its natural rate, restore natural hydrology, and remedy the KHP’s impacts to nutrient dynamics. Pulse flows from Iron Gate Dam could potentially be used to prevent excessive growths of periphyton and aquatic macrophytes; however, this might have unintended consequences as the system is not fully understood. For example, artificially limiting periphyton growth near Iron Gate Dam might the move the zone of poor water quality downstream, merely relocating the problem rather than solving it. DISSOLVED OXYGEN Existing conditions in the Klamath River Dissolved oxygen (D.O.) data for the Klamath River are less robust than for temperature and pH because of the continuous recorders can have problems resulting from fouling of probes that may cause incorrect readings. Continuous data from 2004 are the most reliable because it is the only year in which data were post-processed to correct for bio-fouling of the probes. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 79

Data collected for the Klamath River at various locations from below Iron Gate Reservoir (RM 189.13) to the river mouth (RM 0) between the years 2000 and 2004 show a wide range of conditions. Figure 14 shows the mean daily minimum D.O. for 2000-2004 by river mile and the reference line of 7.0 mg/L on the chart above reflects research showing reduced swimming ability of juvenile chinook salmon (WDOE 2002). Only one location near the mouth of the river at Terwer Creek (RM 5.73) meets the proposed NCRWQCB (2005) standards for D.O., which is a minimum of 8.0 mg/L. All locations near Iron Gate Reservoir show significantly depressed D.O. in 2001 and 2004. The 2004 D.O. daily average minimum for August 2004 shows depressed levels all the way down to the Scott River with average daily minimum D.O. dipping below 6.0 mg/L, well into the stressful ranges for salmonids (Reiser and Bjornn 1979). While monthly mean minimum D.O. levels indicate chronic stress for juvenile salmonids, daily minimum data from some mainstem Klamath River locations show levels dipping more toward acutely low D.O. levels of 5 mg/L. Figure 15 shows daily minimum, average and maximum D.O. above the Scott River. Minimums continue under 6 mg/L into October, which raises concerns about D.O. levels needed for spawning. NCRWQCB proposed D.O. standards for spawning are 8.0 mg/L in redds and 11 mg/L in the water column, values clearly not met according to gauge results.

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Figure 14. The mean daily minimum D.O. for August in various years from 2000-2004 are displayed here with river miles (RM) for location reference. River miles range from the outlet of Iron Gate Reservoir at River Mile (RM) 189.73 to the mouth at RM 0. Data are from the USFWS, Karuk Tribe, Yurok Tribe and USGS. It should be noted that D.O. data for 2000-2003 were not adjusted to correct for biofouling of the probes over the course of a deployment; the only year of D.O. data that have been adjusted to correct for biofouling is 2004. The USFWS (Zedonis 2005), who distributed these data collected by the USFWS, Karuk Tribe, and Yurok Tribe, notes that “the adjusted dissolved oxygen data periodically display a trend of decay through the course of deployment


suggesting that the correction was inadequate to account for all bias.” Figure from Kier Associates 2005). (

Figure 15. This chart shows minimum (red), average (green) and maximum (blue) D.O. values for the Klamath River above the Scott River (RM 142.61) with a threshold that reflects the NCRWQCB (2005) proposed standard for Klamath River D.O. Data are from the USFWS, Karuk Tribe, Yurok Tribe and USGS. Figure from Kier Associates (2005). While data collected by the U.S. Fish and Wildlife Service Arcata Fisheries Office in August of 1997 was anomalous, it bears mention because it likely represents extreme conditions that sometimes occur. WDOE (2002) set acute lethal D.O. limits for warm water species at 3.5-4.0. USFWS crews measured Klamath River D.O. of 3.1 during nocturnal swings on August 9-10, 1997 (Figure 16) and mortality of Klamath small-scale suckers and speckled dace both confirm that conditions at that time had reached acute lethality. Other limnological conditions such as pH and dissolved ammonia were not measured, but may have been cumulatively adding to fish stress and mortality.


Figure 16. USFWS Arcata Fisheries Office measured D.O. levels at night and in early morning hours of August 9-10, 1997 and discovered minimum nocturnal levels of 3.1 mg/L, which are lethal for salmonids according to WDOE (2002). Project effects The KHP has both direct and indirect effects on dissolved oxygen in the Klamath River. The KHP has a direct effect on dissolved oxygen (D.O.) levels in the Klamath River immediately below Iron Gate Dam because during the summer season, the reservoir often releases water with low levels of oxygen (Figure 14). This effect is likely localized in impact, though it is unknown how large the area is. Due to oxygen exchange between the water surface and the air, dissolved oxygen levels should rise once the water is flowing down the river; however, in the Klamath River there is excessive growth of aquatic macrophytes and periphytic algae which causes large diurnal fluctuations in dissolved oxygen levels. Photosynthetic activity by aquatic plant life during the day may cause supersaturated D.O. conditions and respiration at night can cause D.O. declines. To the extent that the project increases nutrient levels, which is still an unsettled question (see discussions in the nutrient section above), it stimulates growth of aquatic macrophytes and periphyton that drive large diurnal swings in D.O., including low D.O. at night. Another unanswered question is what happens to the phytoplankton (free-floating algae) that are flushed from Iron Gate and Copco Reservoirs into the Klamath River below. The discharging of algae from Iron Gate reservoir into the river below has been HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 82

documented (Kann 2006). Whatever the fate of algal cells in the river, they likely have a detrimental effect on dissolved oxygen in the river. If the algal cells survive and continue to grow, then they contribute to diurnal fluctuations of dissolved oxygen. If they die, the microorganisms that decompose them will respire, removing oxygen from the water. Remediation To mitigate KHP impacts to dissolved oxygen, PacifiCorp (2005b) has proposed an oxygen diffuser system for Iron Gate reservoir. If the information presented in the report is correct, it appears that the diffuser would be effective in increasing dissolved oxygen levels in Iron Gate Dam releases. We would like PacifiCorp to provide more detailed information regarding how the diffusion system would affect reservoir chemistry, and provide examples of evaluations of this technology’s effectiveness in other eutrophic reservoirs. While we agree that if this system is put into place, monitoring and testing will be required during installation and operation, additional up front evaluation should be required. Dam removal would eliminate the KHP’s effects on dissolved oxygen levels in the Klamath River. PH Background information Evidence from laboratory studies indicates that any pH over 8.5 is stressful to salmonids and 9.6 is lethal (Wilkie and Wood 1995). Studies show that as water reaches a pH of 9.5, salmonids are acutely stressed and use substantial energy to maintain pH balance in their bloodstream (Wilkie and Wood 1995), while pH in the range of 6.0 to 8.0 is normative. Wilkie and Wood (1995) note that when the gill membranes of bony fishes, including salmonids “are exposed to alkaline water there is an immediate reduction in ammonia excretion rate and a corresponding increase in plasma ammonia concentration.” The direct stress effects of increased pH in the Klamath River are compounded by increasing unionized ammonia, which is triggered by increasing pH in conjunction with typically warm water conditions in summer (see below). Prolonged exposure to pH levels of 8.5 or greater may exhaust ion exchange capacity at gill membranes and lead to increased alkalinity in the bloodstream of salmonids (Wilkie and Wood 1995). This internal shift in chemistry facilitates conversion of internal ammonium to dissolved ammonia (Heisler 1990). In case of extreme pH swings “NH3 and NH4

+ concentrations rise too rapidly and/or approach toxic levels, internal ammonia can ultimately contribute to high pH induced mortality” (Wilkie and Wood 1995). Dissolved ammonia causes a similar diffusion pressure on the gills to high pH as salmonids try to convert NH3 into more benign NH4

+, thus causing loss of H+ ions at the gill membrane. This compounds problems in maintaining pH balance in the bloodstream of juvenile and adult salmonids exposed to both stressors. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 83

Existing conditions in the Klamath River The NCRWQCB (2001) Basin Plan standard for the Klamath River is that pH should not exceed 8.5, but this standard is exceeded on a daily basis across large portions of the river (Figures 16 and 17). Figure 16 shows the average maximum pH during the month of August at all locations monitored on the Klamath River from 2000-2004. The pH rises above levels known to be stressful to salmonids at locations immediately below Iron Gate Dam (RM 189.13) downstream to the mouth of the Shasta River (RM 176.08). The data show considerable variability between sites and between years. The variability of pH between years is reflective of changes in flows, climatological conditions, and other factors, but the consistent exceedance of the NCRWQCB pH standard of 8.5 is an indication of pervasive nutrient pollution and consequently a high probability of problems for fish health.

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Figure 16. Average maximum pH of the Klamath River by river mile showing patterns for the years 2000-2004. The horizontal line shown on the graph is the NCRWQCB (2001) standard for pH. Data are from the USFWS, Karuk Tribe, Yurok Tribe and USGS. Figure is from Kier Associates (2005).


Figure 17. Map showing the percent of summer days in 2004 where maximum pH exceeded 8.5. Data are from Yurok Tribe, Karuk Tribe, and U.S. Fish and Wildlife Service. Figure is from Kier Associates (2005).

Project effects The KHP has both direct and indirect effects on pH in the Klamath River. The KHP has a direct effect on pH levels in the Klamath River immediately below Iron Gate Dam, as during the summer season the reservoir often releases water with high pH (Figure 16). This effect is likely localized in impact, though it is unknown how large the area is. Levels of pH are elevated throughout the Klamath River below Iron Gate Dam (Figures 16 and 17), and it is likely that the pH of water released from Iron Gate Dam does not drive this except for the reach immediately below the dam. Further downstream of the dam, high pH is caused by excessive photosynthesis of aquatic macrophytes and periphytic algae.


To the extent that the project increases nutrient levels, or delays decreases in nutrient levels, which is still an unsettled question (see discussions in the nutrient section above), it stimulates growth of aquatic macrophytes and periphyton that drive large diurnal swings in pH, including high pH during the daylight hours. If the phytoplankton that are flushed out of Iron Gate Reservoir into the Klamath River below continue to photosynthesize, which at this point is unknown, then they contribute to diurnal fluctuations of dissolved oxygen. The Periphyton and Aquatic Macrophytes section above provides additional information on how the KHP encourages growth of periphyton and aquatic macrophytes, and hence increases pH. Remediation Dam removal would eliminate both the KHP’s direct and indirect effects on pH. We are not aware of any way to mitigate the KHP’s impact to pH. AMMONIA TOXICITY Background information Ammonia is a nitrogen-containing compound this is toxic to fish, but is also a nutrient for aquatic plants and algae. Ammonia’s toxicity to fish depends on ammonia concentration, temperature, pH, and duration of exposure (U.S. EPA 1999). As pH and temperature increase, ammonia converts from ammonium ions to unionized or dissolved ammonia that is lethal to salmonids at very low levels. Goldman and Horne (1983) explained that conversion of ammonium to dissolved ammonia is prompted by increasing pH with greater than 38% converted at a pH of 9.0 and a water temperature of 25 O C (Figure 18).


Figure 18. Chart showing the percent conversion of ammonium to dissolved ammonia with increasing pH and water temperature. Data from Goldman and Horne (1983). Existing conditions in the Klamath River Laboratories, which did not have adequately low reporting limits, have processed most nutrient data that have been collected on the Klamath River. Consequently, a sample could be reported as a non-detect, but ammonia levels could be high enough to be acutely toxic to fish, or even lethal. We did not perform the specific calculations required to query available data to determine if the ammonia criteria are being exceeded, as the upcoming Mainstem Klamath TMDL will include ammonia toxicity analysis (St. John. pers. comm.). One of the few datasets with adequate reporting limits for ammonia was the North Coast Regional Water Quality Control Board 104b water quality data from 1996 and 1997. These data show that maximum dissolved ammonia can reach levels well above those recognized as acutely stressful to salmonids (Heisler 1990). Maximum levels of dissolved ammonia for 1996 and 1997 by Klamath River location indicate that problems with this substance may be more pronounced in reaches further downstream from Iron Gate Dam (Figure 19).


Figure 19. The maximum dissolved ammonia (also known as unionized ammonia) levels measured in grab samples collected in 1996 and 1997 show levels in the highly stressful to lethal range for salmonids as far downstream as Ikes Falls near Orleans (RM 65.93). The North Coast Regional Water Quality Control Board collected data as part of the 104b program. Project effects Data from the year 2002 (Kann and Asarian 2005) show that Iron Gate and Copco Reservoirs exhibited substantial negative net retention of ammonia, indicating that both are major sources of ammonia (Figure 20). For the overall April-November 2002 period, net retention in Copco was -44% and Iron Gate was -32%. While the magnitude and timing of ammonia releases likely varies from year to year, it is highly likely that it occurs in all years.


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Figure 20. Percent retention of ammonia by month at Iron Gate and Copco Reservoirs in 2002, by month. Negative retention signifies source, positive retention signifies sink. Retention calculated is as incoming load minus outgoing load, minus change in storage. Retention percentage is calculated as retention divided by incoming load. Chart made from summarizing calculations provided in the appendices of Kann and Asarian (2005). Data originally collected by PacifiCorp and U.S. Fish and Wildlife Service. Although Iron Gate Dam releases substantial ammonia into the Klamath River, much of that ammonia is likely transformed relatively rapidly into nitrate or is taken up by periphyton and aquatic macrophytes. The precise rate of uptake or transformation is unknown and likely varies depending on conditions, but should be investigated. Ammonia releases from Iron Gate Dam represent a substantial localized risk to fish in the vicinity. In addition, ammonia releases from Iron Gate also represent a risk to downstream reaches because if assimilative capacity of periphyton and macrophytes are temporarily diminished (i.e. due to cloudy weather, cold temperatures or turbidity) then ammonia could move downstream intact. This may occur at least occasionally, because high levels of unionized ammonia has been detected far downstream of Iron Gate (figure 19). Even if this occurs infrequently, due to its potential for extreme toxicity, ammonia presents a significant risk to fish health. It should be noted here that ammonia downstream could instead be caused by a phenomenon known as nutrient spiraling, where nutrients are absorbed and then are released (such as when periphyton is scoured or senesces), cascade downstream, break down, and then become available again for growth. Remediation Ammonia accumulates in the hypolimnion of both Copco and Iron Gate reservoirs (PacifiCorp 2004). An oxygenation system could potentially reduce ammonia concentrations in the bottom of the reservoir because in the presence of oxygen HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 89

microorganisms can transform ammonia into nitrate. Such a system could also produce unintended results, such as the gas-bubble disease that has plagued Columbia River salmon management efforts. CYANOBACTERIA AND CYANOBACTERIAL TOXINS Background information Cyanobacteria, also known as blue-green algae, are a diverse group of single-celled aquatic organisms found in surface waters worldwide. Lakes, reservoirs, ponds, and slow-moving rivers are especially well suited to cyanobacteria, and given the right conditions – calm water, light, and abundant nutrients – these organisms can reproduce at a high rate, forming vast blooms in the water. The resulting high cyanobacterial algal concentrations are not only aesthetically unpleasing, but often produce toxins that have been implicated in human health problems ranging from skin irritation and gastrointestinal upset, to death from liver or respiratory failure (Chorus and Bartram 1999, Chorus 2001). Microcystis aeruginosa produces the potent hepatotoxin microcystin and has been demonstrated to occur in the Klamath River system (Kann 2006). These hepatotoxins (liver toxins) are powerful cyclical peptides which disrupt the structure of liver cells, causing cell destruction, liver hemorrhage, liver necrosis, and death. In addition to hepatotoxicity, long-term laboratory animal studies indicate that microcystins act as liver tumor promoters and teratogens (Falconer et al. 1988). Microcystin poisoning has been implicated in the largest number of cyanobacteria-associated animal deaths worldwide, and enough work has been done, both with rodents and pigs, on microcystin effects at various levels of exposure, that the World Health Organization (WHO) has issued a provisional guideline of 1 μg/L for microcystin concentration in drinking water. With actual microcystin concentration data frequently unavailable, alert level guidelines based on cell counts have been established for Microcystis (as well as other cyanobacteria) blooms in drinking and recreational waters (Yoo et al. 1995, Chorus and Bartram 1999). Although human health effects of toxins from the blue-green algae Microcystis aeruginosa are better studied, fish health effects have also been recently researched (Zambrano and Canelo 1995, Wiegland and Pflugmacher 2005), including effects on salmonids (Tencalla et al. 1994, Bury et al. 1996; Fischer et al. 2000, Best et al. 2003). These effects are discussed here because there is evidence that hepatotoxins created by Microcystis are a threat to fish health independently, and may act synergistically with other water quality problems (i.e. pH) in causing cumulative stress or in contributing to immunosuppression and subsequent outbreaks of fish disease epidemics. Microcystin toxins accumulate in the liver where they disrupt many different liver enzymes and ultimately cause the liver to break down (Fischer et al., 2000). Algae grazing fish species may be the most susceptible to microcystin poisoning, but other fish may ingest whole Microcystis cells or breakdown products from the water column (Wiegland and Pflugmacher 2005). In laboratory experiments, rainbow trout were found to excrete microcystin toxins in bile fluids when exposed to them orally. The toxins HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 90

caused increased drinking in this species and increased water in the gut, which was a sign of osmoregulatory imbalance and could promote diffusion of toxins into the blood (Best et al., 2003). Tencalla et al. (1994) noted that large-scale fish kills around the world have resulted from microcystin poisoning. They postulated that a 60 g rainbow trout would only have to ingest 0.1-0.4 g of algae (wet weight) or 0.2-0.6% of its body weight to experience massive liver damage. Bury et al. (1996) studied brown trout exposed to sublethal levels of microcystin toxins and found greatly altered blood cortisol levels indicating acute stress and reduced immunosuppression. This is a concern in the mainstem Klamath River because of the recognized fish health problems (Foott and Stone, 2003; Nichols and Foott, 2005), and the potential for additional diminishment of resistance to disease caused by microcystin exposure of juvenile salmonids. Existing conditions in the Klamath River Kann (2006) provides a summary of four datasets that provide information about the distribution and abundance of Microcystis aeruginosa (MSAE) in the Klamath River basin. These include data from the Klamath Tribes in 1990-1997, PacifiCorp in 2002-2004, Karuk Tribe/State Water Resource Control Board (SRWCB) in 2005, and Yurok Tribe/U.S. Fish and Wildlife Service (USFWS) in 2005. The Klamath Tribes’ 1990-1997 data showed that while MSAE is found in Upper Klamath Lake and Agency Lake, it was only rarely detected in the outlet to Upper Klamath Lake. PacifiCorp’s data showed that MSAE was only detected in twice (August 21, 2003 and September 10, 2002) in the Klamath River above Copco (river mile 206.42), but then was common in Iron Gate and Copco Reservoirs. In Karuk Tribe/SWRCB data from 2005, MSAE and microcystin toxin were never detected at the station above Copco Reservoir, but were common in Iron Gate and Copco Reservoirs and in the Klamath River at the outlet of Iron Gate Dam. Yurok/USFWS data from 2005 showed that MSAE and microcystin toxin were found in the Klamath River all the way from Iron Gate Dam to the Klamath estuary. Based on those results, Kann (2005) concludes:

Taken together these data provide compelling evidence that Copco and Iron Gate Reservoirs are providing ideal habitat for MSAE; increasing concentrations dramatically from those upstream, and exporting MSAE to the downstream environment.

Project effects The results described above from multiple datasets and summarized by Kann (2005) indicate that Iron Gate and Copco Reservoirs were almost certainly for the responsible for the high levels of MSAE and microcystin toxin detected in the Klamath River between Iron Gate Dam and the estuary.


Kann (2005) described the potential for Iron Gate and Copco Reservoirs to contribute to downstream blooms of MSAE:

In areas where turbulent diffusivity may decrease as rivers widen and increase in depth, or such as would occur in backwater areas, the potential also exists for MSAE blooms in slow-moving riverine environments as well …Given the tens of thousands of MSAE cells introduced to the lower-Klamath River from Copco and Iron Gate Reservoirs above, the potential for recurring blooms downstream increases as slower-moving water is encountered. For example, as described above, MSAE cell concentration exceeded 1.3 million cells/ml in a backwater area near the confluence of Coon Creek nearly 100 miles downstream from Iron Gate Dam.

With dam removal, although Microcystis might persist at low levels in the Klamath River’s quiet backwaters or perhaps in the Klamath estuary, its abundance would likely be reduced many fold. The reason is that its inoculant source (Iron Gate and Copco Reservoir) would be reduced by orders of magnitude, so that even in a suitable MSAE habitat such as a quiet backwater, blooms would take longer to develop because they would start from fewer cells, and cells would have less of a chance of dispersing to suitable habitats. California’s water quality standard for toxic substances states, “All waters shall be maintained free of toxic substances in concentrations that are toxic to, or that produce detrimental physiological responses in, human, plant, animal, or aquatic life.” (NCRWQCB, 2001). To the extent that creation of the KHP reservoirs resulted in formation of habitat conditions ideal for Microcystis, with subsequent increased microcystin concentration in the waters of the Klamath River, operation of the KHP may be violating California’s toxic substances water quality standard. Remediation As described above, Iron Gate and Copco Reservoirs provide ideal habitat for MSAE. Dam removal would eliminate these reservoirs, dramatically reducing available habitat for MSAE. Without the KHP reservoirs, MSAE might persist in the Klamath River, but it would likely be at much lower levels than found in 2005, for reasons described above. TASTE AND ODOR COMPOUNDS Background information The issue of taste and odor compounds may seem at first like a minor issue, but in the Klamath Basin, it is an important one. Fish growing in water containing taste and odor compounds can take these compounds into their tissues. Off-flavored fish can adversely affect recreational fishing because eating such fish becomes less desirable. This, in turn, can have negative economic effects on recreational economies, including bait and HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 92

tackle sales and boat and cottage rentals (EPA 1986). Several Native American Tribes in the Klamath basin have subsistence fisheries, which is another reason why taste and odor compounds are important issues. A likely source of potential taste and odor compounds in the Klamath River is algae. As it grows and decays, algae can produce undesirable tastes and odors in water (EPA 1996 and Droste 1997). Smith and deNoyelles (2001) provide a summary of the background and history of taste-and-odor compounds in surface water, as does Mau et al. (2004). Many algal species are capable of producing tastes and odors, including various Bacillariophyta, Chlorophyta, Cryptophyta, and Actinomycetes. Taste and odors vary between species. Species causing "grassy" or "musty" odors include the diatoms Melosira and Synedra, as well as the Cyanobacteria Anabaena (Palmer 1977). Diatoms that can cause "fishy" odors include Asterionella, Cyclotella, and Chlamydomonas (Palmer 1977). Cyanobacteria Oscillatoria spp. and Lyngbya limnetica are capable of producing “musty odor” (Palmer 1997). Other species know to produce taste and odor compounds include the Cyanobacteria Aphanizomenon. Actinomycetes are moldlike bacteria than can break down organic matter and produce many taste and odor compounds including geosmin, an earthy-smelling byproduct which is also produced by Cyanobacteria (Droste 1997). Some of the most severe taste and odor problems have been associated with blooms of cyanobacteria (Mau et al. 2004). Two chemical compounds found within certain species of cyanobacteria, geosmin and 2-methylisoborneol (MIB), are responsible for many of the taste and odor problems associated with cyanobacteria blooms (Gerber, 1969; Tabachek and Yurkowski, 1976). Existing conditions in the Klamath River While we are not aware of any quantitative data regarding the types and concentrations of taste and odor compounds in the Klamath River, it is widely recognized that salmon caught on the middle Klamath River (between Iron Gate Dam and the Trinity River) have poor odor and taste. Staff of the Quartz Valley Indian Reservation eloquently stated this during a meeting with FERC (2004):

“Around here, when people say that they got salmon, the first question that you ask is where did you get it from? If they got it up river, you don't want to eat it. People that don't know, eat it. But people that know get it farther down.”

PacifiCorp conducted a survey of recreational users in the KHP area and results are included in Water Resources Final Technical Report Appendix 13a Klamath Water Quality/Aesthetics Survey Responses (PacifiCorp 2004). Thirty-six percent of recreational users indicated that water quality affected their visit to the Klamath River and many respondents commented on the excessive algae, green water, foam, suds,


and bad odors found in the KHP reservoirs and river reaches. Comments included the following: - “Bad smell this year” (regarding Keno and Lake Ewauna) - “Slimy, green, foamy – yuck” (regarding Copco/Lower Klamath) - “Extremely filthy (also dead fish everywhere)” (regarding J.C. Boyle) Humboldt State University graduate students are conducting studies of the relationships between nutrients, Actinomycetes, and geosmin in the mainstem Klamath River but have not published their results yet (Gearheart, pers. comm.). Project effects: Data on taste and odor compounds is lacking in the Klamath River, but analysis of phytoplankton and nutrient data, combined with information about taste and odor compounds from literature derived in other locations, suggests that the KHP is likely increasing taste and odor compounds in the Klamath River. Each year, KHP reservoirs such as Iron Gate and Copco host massive algae blooms. Organic matter (likely live and dead algae) can be flushed downstream in the Klamath River below (Kann and Asarian 2005). These blooms are likely contributing to taste and odor problems both directly through metabolic byproducts of the algae, as well and indirectly through increasing organic matter, which can later be decomposed by Actinomycetes to produce geosmin and other taste and odor compounds. In addition, anaerobic conditions in the bottoms of the reservoirs may also produce taste and odor compounds. Remediation As described above in the nutrients section, copper-based algaecides could potentially be used to reduce algal growth and hence reduce taste and odor compounds, but we strongly discourage this approach due to potential for unintended downstream consequences. Removing KHP dams and reservoirs would reduce algal production and anaerobic conditions, likely reducing taste and odor compound production. As discussed in the nutrients section above, it would also likely reduce levels of nutrients and organic matter in the Klamath River downstream, which should reduce algal growth as well as reduce the amount of geosmin produced by Actinomycetes (which feed on organic matter). Taste and odor-causing compounds are often volatile and can be removed to a significant extent by aeration (Droste 1997). Adding oxygen to water can improve the taste of water to a limited extent (Droste 1997). Dam removal would replace anaerobic reservoirs with many miles of a free-flowing river that has a much higher surface area to volume ratio than the reservoirs, which would allow for more replenishment of oxygen. In addition, free-flowing rivers feature naturally occurring gravity-powered aeration features known as riffles, which further serve to oxygenate the water. The increase in surface area to volume ratio and increase in the number of riffles would likely result in


more aeration and hence more removal of taste and odor compounds from the waters of the Klamath River. F ISH PARASITES Background information In recent years, myxozoan parasites have received increasing attention in the Klamath River, especially for their role in causing fish kills of juvenile salmonids. The two that have been most closely studied are Ceratomyxa shasta and secondarily Parvicapsula minibicornis. The life cycle of C. shasta utilizes two different hosts: the freshwater polychaete worm Manaynukia speciosa and a salmonid (Figure 21). Bartholomew (2006) recently discovered that Parvicapsula minibicornis also uses the same polychaete host.

A D

E

B

F

C G

Figure 21. Life cycle of Ceratomyxa shasta showing release of the myxospore stage from the infected fish, the polychaete alternate host, and release of the alternate actinospore stage from the polychaete. A. released actinospores, B. electron micrograph of actinospores in the polychaete, C. polychaete, D. infected fish, E. histological section of infected intestine, F. trophozoite stages, G. myxospore (Bartholomew et al. 1997). Existing conditions in the Klamath River C. Shasta was first detected in the Klamath River in the early 1990s and was first identified as being a serious fish health issue in 1995. The recent high incidence of C. Shasta in the Klamath River may be due to an increase in polychaete population is caused by an increase in polychaete habitat (Stocking and Bartholomew, 2004). Unpublished data from recent surveys on the Klamath River have shown that the polychaete’s primary habitat is sand with fine benthic organic matter (Stocking 2006). HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 95

Its secondary habitat is dense beds of Cladophora, a filamentous green algal species. There are some notable differences between these two habitats. Polychaetes living on the sand with fine benthic organic matter substrate are restricted to low-velocity areas, whereas polychaetes can exist in Cladophora in areas with higher water velocities (Stocking 2006). In addition, sand with fine benthic organic matter is a less stable substrate than Cladophora. For example, Stocking (2006) sampled an extremely large and dense population of polychaetes at Tree of Heaven (approximate river mile 170) in March 2005. When Stocking returned to sample after a high-flow event (discharge below Iron Gate Dam peaked at 5380 cubic feet per second on May 18) in May 2005, much of the organic matter was gone and all polychaetes had disappeared (presumably both had been washed downstream). In contrast, polychaete populations in Cladophora beds remained intact. To date, there has been no systematic effort to map the distribution and abundance of Cladophora in the Klamath River and its tributaries. Cladophora distribution in the Klamath River appears to be patchy. When present it often covers large areas with a dense mat (Stocking, pers. comm.). Stocking (pers. comm.) says that Cladophora is most common between Iron Gate (river mile 190) and Happy Camp (approximate river mile 100), and he has not seen it downstream of the Klamath’s confluence with the Trinity (river mile 44). A recent unpublished study examined the rates of C. shasta and P. minibicornis infectivity in their polychaete host M. speciosa in the Klamath River from Keno Reservoir to China Point near Happy Camp (Stocking 2006). The study found that in the year 2005, the sites with highest C. shasta infection prevalence in polychaetes were the Tree of Heaven (approximately river mile 170) and Interstate 5 (approximately river mile 179). The most likely explanation for this high infection prevalence at these sites is their proximity to the salmon spawning grounds below Iron Gate Dam. Returning adult salmon can become infected with C. shasta as they move upriver. When they spawn and die, the C. shasta myxospores contained inside them are released and can infect polychaetes. Ceratomyxa shasta causes major problems for the health of juvenile salmonids in the Klamath River. C. Shasta infection rates are extremely high and, in many years, results in the death of significant portion of the juvenile salmonids in the Klamath River. Nichols and Foott (2005) estimated that in 2004, 45% of juvenile fall-run chinook salmon were infected with C. Shasta, 94% of the population was infected with P. minibicornis. The majority of the C. Shasta infected fish would not survive, and the impact of a loss of that many fish could rival the 2002 adult fish-kill where over 33,000 adult salmon died. Foott (pers. comm.) noted that C. Shasta parasite loads are so high in the Klamath River that even healthy fish with active immune systems can be overwhelmed. To reduce the incidence of C. Shasta infection in the Klamath River, it may be insufficient to improve physical water quality temperature, pH and D.O. alone to reduce fish stress. It also may require a reduction in parasite loads. Reducing parasite loads could likely be achieved by reducing populations of the polychaete. This could likely be achieved by HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 96

reducing available habitat for the polychaete. Reducing the amount of organic matter in the Klamath River would reduce the amount of the polychaete’s primary habitat (sand with fine benthic organic matter). As explained above in the Periphyton section, green algae such a Cladophora are more common in streams with high nutrient concentrations, so reducing the amount of nutrients in the Klamath River would likely lead to a reduction in the amount of Cladophora (the polychaete’s secondary habitat). In a recent unpublished study, the Karuk Tribe collected water samples biweekly at many sites between Iron Gate Dam and the Klamath estuary from May through September (Bartholomew 2006). A technique known as QPCR was used to quantify the amount of C. Shasta DNA in the water samples. Known quantities of C. Shasta spores were also processed with QPCR, which allows development of quantitative relationship between QPCR results and the number of spore in a sample. The biological significance (to fish) of specific spore concentrations is still unknown at this time, but this knowledge will be developed over time by performing QPCR on water samples in the same locations as sentinel fish studies are being conducted. Even in the absence of accurate knowledge of the biological significance of spore counts, knowing spore counts is still useful because it allows comparison of the relative exposure risk between sites and time periods. Unpublished preliminary analyses of the 2005 QPCR sampling results suggested some trends (Bartholomew 2006). Spore counts were generally highest in June and July, except for sites downstream of the Trinity River where there were never many spores detected at any time during the season. The longitudinal pattern was that spore counts were right below Iron Gate, then spiking to high (approximately 10-20 spores/L) at the Klamath above the Shasta, and then decreasing as water flowed downstream past each successive monitoring station, with the Klamath River above the Scott River and Klamath River at Seiad Valley still having relatively high concentrations. Project effects The upstream ends of KHP reservoirs have the largest populations of polychaetes discovered anywhere in the Klamath system (Stocking 2006). Polychaetes are not found in other portions of the reservoirs, likely because they need oxygen (Stocking, pers. comm.) and water quality in the reservoirs is so poor that the depths are anaerobic and hence polychaetes cannot survive. On extreme high-flow events, polychaetes could potentially be flushed from the upper ends of the reservoirs into the river below, though it is unknown if this occurs. It has been documented that the reservoirs can periodically release pulses of organic matter downstream (Kann and Asarian 2005). When this organic matter settles in depositional zones of the Klamath River, it provides ideal habitat for C. shasta’s polychaete host M. speciosa. This likely contributes to higher polychaete populations, higher spore loads of C. shasta in the water column, C. shasta infection in salmonids, and hence salmonid disease and death.


As discussed in the Periphyton section above, the KHP reservoirs disrupt downstream transport of gravel, leading to substrate coarsening and armoring of the streambed below Iron Gate Dam, which favors the establishment of green filamentous algae such as Cladophora. Additionally, as discussed above, the KHP reservoirs also provide a stable hydrologic regime by reducing peak flows, which also encourages periphyton growth, including Cladophora. These two KHP-driven mechanisms likely contribute to larger populations of C. shasta’s polychaete host M. speciosa by expanding the quantity of its secondary habitat (Cladophora beds). This likely contributes to higher polychaete populations, higher C. shasta spore loads in the water column, C. shasta infection in salmonids, and hence salmonid disease and death. Lastly, Iron Gate Dam (river mile 190) is a complete barrier to fish. This causes massive aggregations of spawning fish in the mainstem Klamath River below the dam (Figure 6). As noted above, the highest rates of C. shasta infection in polychaetes were found at Tree of Heaven (approximately river mile 170) and Interstate 5 (approximately river mile 179). These high infection rates may be due to Iron Gate Dam causing a blockage in salmon migration. If the dams were removed, or some other type of fish passage provided, the salmon would likely spawn over a more dispersed area, and there would not be massive release of C. shasta spores that occurs with spawning and death thousands of fish in a relatively small area. As discussed above in the Temperature, pH, Dissolved Oxygen, and Ammonia Toxicity sections above, the KHP is detrimental to physical and chemical water quality, which contributes to fish stress and immunosuppression, increasing chances of infection and disease. Remediation Removal of KHP dams would reverse the KHP effects described above, including reversing the KHP-driven expansion of habitat for C. shasta’s polychaete host M. speciosa by reducing the amount of organic matter and Cladophora in the Klamath River. With dam removal or provision of fish passage, the salmon would likely distribute salmon spawning over a larger area, reducing C. Shasta spore counts. Dam removal would also improve water temperature, pH, dissolved oxygen, and ammonia levels, which would reduce salmonid stress and hence help restore salmonid immune systems. For these reasons, it is likely that dam removal would contribute to enhanced fish health and lower incidences of myxosporean parasite diseases in Klamath River salmonids. NEED FOR URGENT ACTION Recent fish health studies of the Klamath River by the U.S. Fish and Wildlife Service California-Nevada Fish Health Center (Nichols and Foott, 2005) indicate a high incidence of disease in juvenile salmonids:


“We estimated that 45% of the population was infected with C. shasta and 94% of the population was infected with P. minibicornis. The prognosis for P. minibicornis infection by itself is not well understood. The high incidence of dual myxozoan infection (98% of C. shasta infected fish), and associated pathology suggests that the majority of the C. shasta infected juvenile Chinook would not survive.”

The loss of 45% or more of juvenile downstream migrants to disease shows epidemics of disease that threaten persistence of Pacific salmon stocks in the Klamath River. Recent record low escapements of spring (Figure 22) and fall (Figure 23) fall chinook to the Salmon River and two consecutive record lows in the Scott River basin (Figure 24) in 2004 and 2005 suggest that mainstem Klamath River water quality is precipitating a basin wide chinook salmon stock collapse. Higgins et al. (1992) discussed the risk of extinction of northwestern California Pacific salmon stocks and discussed minimum viable population sizes:

“When a stock declines to fewer than 500 individuals, it may face a risk of loss of genetic diversity which could hinder its ability to cope with future environmental changes (Nelson and Soule 1987). A random event such as a drought or variation in sex ratios may lead to extinction if a stock is at an extremely low level (Gilpin and Soule 1990). The National Marine Fisheries Service (NMFS, 1987) acknowledged that, while 200 adults might be sufficient to maintain genetic diversity in a hatchery population, the actual number of Sacramento River winter run chinook needed to maintain genetic diversity in the wild would be 400-l,100.”

The populations of fall chinook in the Salmon River and Scott River have plummeted to all time lows for two years running despite favorable or average ocean conditions (Collison et al. 2003) and wet years with at least average flows. These populations have some additional ability to rebound without loss of genetic diversity because chinook spawn at different ages, but the low adult returns should be viewed with alarm. Several mainstem Klamath River water quality parameters approach or exceed lethal conditions for salmonid juveniles below the Scott and Salmon Rivers throughout summer as described by Kier Associates (2005) and above in this document. High water temperature currently couples with nutrient enrichment (likely due at least in part to KHP reservoirs) that sets off nutrient spiraling and high rates of photosynthesis that lead to high pH, depressed D.O. and periodic problems with highly toxic dissolved ammonia. To compound those factors even more, the recently discovery of the toxic algae Microcytis aureginosa indicates yet another threat to salmonids (and humans). When all these indicators are considered together, it becomes clear that the Klamath River is in serious trouble and that the dismantling of the KHP is an essential step on the road to recovery for the river and its peoples.


Figure 22. Salmon River fall chinook escapement plummeted in 2004 and 2005 to the lowest escapement on record since 1978 two years in a row. Data from CDFG (2006).

Figure 23. Salmon River spring chinook fell to an all time low in 2005. SRRC. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 100

Figure 24. Scott River fall chinook escapement shows a similar trend to Salmon River populations, with both 2004 and 2005 well below average and the lowest years on record


Literature Cited Bartholow, J.M., 2005. Recent Water Temperature Trends in the Lower Klamath River,

California. North American Journal of Fisheries Management 25: 152–162, 2005. Bartholomew, J. L., M. J. Whipple, D. G. Stevens and J. L. Fryer. 1997. The life cycle of

Ceratomyxa shasta, a myxosporean parasite of salmonids, requires a freshwater polychaete as an alternate host. American Journal of Parasitology. 83:859-868.

Bartholomew, J. L. 2006. Presentation at the 2006 Klamath Fish Health Workshop on

February 2, 2006 at Humboldt State University, Arcata, California. Belchik, M. 1997. Summer locations and salmonid use of cool water areas in the Klamath

River - Iron Gate Dam to Seiad Creek 1996. Yurok Tribal Fisheries Program. Klamath, CA. 15 pp. Available online at: <http://www.krisweb.com/biblio/klamath_ytfp_belchik_1997_refugia.pdf>. Accessed 2006 12 February.

Best, J.H., F.B. Eddy, and G.A. Codd. 2003. Effects of Microcystis cells, cell extracts and

liposaccharides on drinking and liver function in rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology, Vol. 64, No. 4: 419-426.

Biggs, B.J.F. 2000. New Zealand Periphyton Guideline: Detection, Monitoring, and

Managing Enrichment of Streams. Prepared for Ministry of Environment. NIWA, Christchurch.

Bury, N.R., F.B. Eddy, and G.A. Codd. 1996. Stress Responses of Brown Trout, Salmon

trutta L., to the Cyanobacterium, Microcystis aeruginosa. Environmental Toxicology and Water Quality. Vol. 11 (1996) 187-193.

California Department of Fish and Game (CDFG). 2003. September 2002 Klamath River

Fish Kill: Preliminary analysis of contributing factors. CDFG, Region 1, Redding, CA. 67 pp.

California Energy Commission. 2003. Preliminary assessment of energy issues associated

with the Klamath Hydroelectric Project. California Energy Commission Report. Prepared for the California Resources Agency and State Water Resources Control Board l.

Chorus I, editor. 2001. Cyanotoxins: occurrence, causes, consequences. Springer-Verlag:

Berlin. Chorus I, Bartram, J, editors. 1999. Toxic cyanobacteria in water. E & FN Spon: London. Chorus, I, and M. Cavalieri. 2000. Cyanobacteria and algae. Pages 219-271 in: J. Bartram

and G Rees, editors. Monitoring Bathing Waters: a practical guide to the design and implementation of assessments and monitoring programmes. World Health Organization Report. E & FN Spon, London and New York.


http://www.krisweb.com/biblio/klamath_ytfp_belchik_1997_refugia.pdf

City of Klamath Falls (RMI). 1986. Application for license, Salt Caves Hydroelectric Project, FERC No. 10199. Submitted to the Federal Energy Regulatory Commission by the City of Klamath Falls.

Deas, M. 2004. Klamath River Water Quality Analysis; Link Dam to the Pacific Ocean.

Watercourse Engineering, Inc. Powerpoint presentation to Water Quality Group stakeholders, March 4, 2004.

Deas, M. 2004. Powerpoint presented to PacifiCorp’s Water Quality Work Group meeting in

Yreka, CA on November 23, 2004. Droste, R. 1997. Theory and practice of water and wastewater treatment. John Wiley and

Sons, Inc. New York. 800pp. Edwards, R.T. 1998. The Hyporheic Zone. Pages 399-429 In R.J. Naiman and R.E. Bilby,

eds. 1998. River Ecology and Management. Springer-Verlag New York, Inc. New York, 705 pp.

Eilers, J.M. 2005. Periphyton in Selected Sites of the Klamath River, California. Prepared for

Tetra Tech, Inc. Fairfax, VA by J.M. Eilers MaxDepth Aquatics, Inc. Bend, OR. 20 p. Falconer et al. 1999. Safe levels and safe practices. Pages 155-177 in: I. Chorus and J.

Bartram, editors. Toxic Cyanobacteria in water: a guide to their public health consequences.World Health Organization Report. E & FN Spon, London and New York.

Federal Energy Regulatory Commission. 2004. Hearing before the Federal Energy

Regulatory Commission in the matter of the Klamath Hydroelectric Project No P-2082. December 15, 2004 at Quartz Valley Indian Community, Fort Jones, California.

Fischer, W.J., B.C, Hitzfeld, F. Tencalla, J.E. Eriksson, A. Mikhailov, and D.R. Dietrich. 2000.

Microcystin-LR Toxicodynamics, Induced Pathology, and Immunohistochemical Localization in Livers of Blue-Green Algae Exposed Rainbow Trout (Oncorhynchus mykiss). Toxicological Sciences, Vol. 54: 365-373.

Fishpro. 2000. Fish passage conditions on the Upper Klamath River. Submitted to the Karuk

Tribe and PacifiCorp. Port Orchard, WA. Foott J.S., R. Harmon, and R. Stone. 2003. FY2002 Investigational Report: Ceratomyxosis

resistance in juvenile chinook salmon and steelhead trout from the Klamath River. U. S. Fish and Wildlife Service, California- Nevada Fish Health Center. Anderson, CA. 25 pp. Available online at: <http://www.krisweb.com/biblio/klamath_usfws_foottetal_2003_cerat.pdf> Accessed 2006 12 February.

Foott J.S., T. Martinez, R. Harmon, K. True, B. McCasland, C. Glace, and R. Engle. 2002.

FY2001 Investigational Report: Juvenile Chinook Health Monitoring in the Trinity River, Klamath River, and estuary. June-August 2001. U. S. Fish and Wildlife Service, California- Nevada Fish Health Center. Anderson, CA. 34 pp. Available online at: <http://www.fws.gov/canvfhc/reports/files/Klamath & Trinity River/Juvenille Chinook


http://www.krisweb.com/biblio/klamath_usfws_foottetal_2003_cerat.pdf

http://www.fws.gov/canvfhc/reports/files/Klamath%20&%20Trinity%20River/Juvenille%20Chinnook%20Health%20Monitoring%20in%20the%20Trinity%20and%20Klamath%20Rivers%20(2001).PDF

Health Monitoring in the Trinity and Klamath Rivers (2001).PDF> Accessed 2006 12 February.

Fortune, J.D., A.R. Gerlach, and C.J. Hanel. 1966. A study to determine the feasibility of

establishing salmon and steelhead in the upper Klamath basin. Oregon State Game Commission and Pacific Power and Light Company.

Gearheart, Robert. Personal Communication. Professor of Environmental Engineering at

Humboldt State University. Gerber, N.N., 1969, A volatile metabolite of actinomycetes, 2-methylisoborneol: Journal of

Antibiotics, v. 22, p. 508. Gilpin, M.E. and M.E. Soule. 1990. Minimum Viable Populations: Processes of Species

Extinction. In: M. Soule (ed) Conservation Biology: The Science of Scarcity and Diversity University of Michigan Press. pp 19-36.

Goldman, C.R. and A.J. Horne. 1983. Limnology. McGraw-Hill, Inc. New York. 464 pp. Guillen, G. 2003. Klamath River fish die-off, September 2002: Causative factors of mortality.

Report number AFWO-F-02-03. U.S. Fish and Wildlife Service, Arcata Fish and Wildlife Office. Arcata, CA. 128 pp.

Gutermuth, B., C. Watson, and J. Kelly. 2000. Link River hydroelectric Project (Eastside and

Westside powerhouses) final entrainment report, March 1997 – October 1999. Cell Tech Research and Development and PacifiCorp. Portland, OR. 127 pp.

Hecht, B., and G. R. Kamman. 1996. Initial Assessment of Pre- and Post-Klamath Project

Hydrology on the Klamath River and Impacts of the Project on Instream Flows and Fishery Habitat. Balance Hydrologics., Inc. March.

Heisler, N. 1990. Mechanisms of Ammonia Elimination in Fishes. In J.P. Truchot and B.

Lahlou (eds) Animal Nutrition and Transport Processes (Chapter 2) in Comparative Physiology (Vol. 6), pp 137-151.

Higgins, P.T., S. Dobush, and D. Fuller. 1992. Factors in Northern California Threatening

Stocks with Extinction. Humboldt Chapter of American Fisheries Society. Arcata, CA. 25p.

Holmes, R. M., J. B. Jones, Jr., S. G. Fisher, and N. B. Grimm. 1996. Denitrification in a

nitrogen-limited stream ecosystem. Biogeochemistry 33:125-146. Horner, R. R., E. B. Welch, and R. B. Veenstra. 1983. Development of nuisance periphytic

algae in laboratory streams in relation to enrichment and velocity. In: Periphyton of Freshwater Ecosystems: Proceedings of the First International Workshop on Periphyton of Freshwater Ecosystems. R. G. Wetzel (ed.). Developments in Hydrobiology Series, Vol. 17. Kluwer, Boston. pp. 21-134.

Huisman, J. et al. 2004. Changes in turbulent mixing shift competition for light between

phytoplankton species. Ecology 85(11): 2960-2970. HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 104

http://www.fws.gov/canvfhc/reports/files/Klamath%20&%20Trinity%20River/Juvenille%20Chinnook%20Health%20Monitoring%20in%20the%20Trinity%20and%20Klamath%20Rivers%20(2001).PDF

Hunter, M. A. 1992. Hydropower flow fluctuations and salmonids: a review of the biological effects, mechanical causes, and options for mitigation. State of Washington Department of Fisheries. Technical Report 119. Olympia, WA.

Institute For Natural Systems Engineering (INSE). 1999. Evaluation of interim instream flow

needs in the Klamath River: Phase I final report. Prepared for the Department of Interior. 53 p. plus appendixes.

Kann, J. 2006. Technical memorandum: Microcystis aeruginosa Occurrence in the Klamath

River System of Southern Oregon and Northern California. Prepared for the Yurok Tribe Environmental and Fisheries Programs by Aquatic Ecosystem Sciences LLC, Ashland, Oregon. Available online at: <http://www.yuroktribe.org/departments/ytep/documents/KannFinalYurokMsaeTechMemo2-3-06.pdf> Accessed 2006 12 February.

Kann, J. and E. Asarian. 2005. 2002 Nutrient and Hydrologic Loading to Iron Gate and

Copco Reservoirs, California. Kier Associates Final Technical Report to the Karuk Tribe Department of Natural Resources, Orleans, California. 59pp + appendices. Available online at: <http://www.krisweb.com/ftp/KlamWQdatabase/Copco_IG_Budgets.zip> Accessed 2006 12 February.

Kanz, R. 2005. Klamath River Hydroelectric Project Reservoir Water Quality Dynamics Study Water Quality Cooperative Agreement/Grant Application. State Water Resources Control Board, Sacramento, CA. 6 pp. Kier Associates. 1999. Mid-term evaluation of the Klamath River Basin Fisheries

Restoration Program. Sausalito, CA. Prepared for the Klamath River Basin Fisheries Task Force. 303 pp. Available online at: <http://www.krisweb.com/biblio/klamath_usfws_kierassc_1999_evaluation.pdf> Accessed 2006 12 February.

Kier Associates. 2005. Draft Nutrient Criteria for the Klamath River on the Hoopa Valley

Indian Reservation. Prepared for the Hoopa Valley Tribal Environmental Protection Agency. Kier Associates, Mill Valley and Arcata, California.

McCullough, D. A. 1999. A review and synthesis of effects of alterations to the water

temperature regime on freshwater life stages of salmonids, with special reference to chinook salmon. Published as EPA 910-R-99-010 . Prepared for the U.S. Environmental Protection Agency (EPA), Region 10. Seattle, Washington. 291 pp. Available online at: <http://www.krisweb.com/biblio/gen_usepa_mccullough_1999.pdf> Accessed 2006 12 February.

McIntosh, B. A. and H. W. Li. 1998. Abstract and other information regarding the Final report

- Klamath Basin Pilot Project: Coldwater refugia study and videography. Oregon State University. Available online at: <http://www.krisweb.com/biblio/klamath_osu_macintosh_1998_coldwater/start.htm> Accessed 2006 12 February.

HOOPA FISHERIES COMMENTS AND PRELIMINARY 10(a) RECOMMENDED TERMS AND CONDITIONS

Klamath Hydroelectric Project, FERC No. 2082 March 29, 2006 105

http://www.yuroktribe.org/departments/ytep/documents/KannFinalYurokMsaeTechMemo2-3-06.pdf

http://www.yuroktribe.org/departments/ytep/documents/KannFinalYurokMsaeTechMemo2-3-06.pdf

http://www.krisweb.com/ftp/KlamWQdatabase/Copco_IG_Budgets.zip

http://www.krisweb.com/biblio/klamath_usfws_kierassc_1999_evaluation.pdf

http://www.krisweb.com/biblio/gen_usepa_mccullough_1999.pdf

http://www.krisweb.com/biblio/klamath_osu_macintosh_1998_coldwater/start.htm

Mau, D.P., Ziegler, A.C., Porter, S.D., and Pope, L.M., 2004, Surface-water-quality conditions and relation to taste-and-odor occurrences in the Lake Olathe watershed, northeast Kansas, 2000–02: U.S. Geological Survey Scientific Investigations Report 2004–5047, 95 p. Available online at: <http://permanent.access.gpo.gov/waterusgsgov/water.usgs.gov/pubs/sir/2004/5047/pdf/sir2004.5047.pdf> Accessed 2006 12 February.

National Marine Fisheries Service. 1987. Endangered and threatened species, winter run

chinook salmon. Federal Register 52: 604 I-6048. National Research Council (NRC). 2004. Endangered and threatened fishes in the Klamath

River basin: causes of decline and strategies for recovery. Committee on endangered and threatened fishes in the Klamath River Basin, Board of Environmental Toxicology, Division on Earth and Life Studies, Washington D.C. 424 pp. Available online at: <http://www.krisweb.com/biblio/klamath_nsa_nrc_2003.pdf> Accessed 2006 12 February.

Nelson, K. and M. Soule. 1987. Genetic Conservation of Exploited Fishes. In: N. Ryman

and F.Utter (eds). Population Genetics and Fisheries Management University of Washington Press. Seattle, WA..

Nicholas, J.W. and D.G. Hankin. 1988. Chinook salmon populations in Oregon coastal river

basins. Descriptions of life histories and assessment of recent trends in run strengths. Funded by Oregon Department Fish and Wildlife. Oregon State University Extension Service. Corvallis, OR.

Nichols, K. and J.S. Foott. 2005. FY2004 Investigational report: Health Monitoring of

Juvenile Klamath River Chinook Salmon. U.S. Fish & Wildlife Service California-Nevada Fish Health Center, Anderson, CA.

North Coast Regional Water Quality Control Board. 2001. Water Quality Control Plan for the

North Coast Region. Staff report adopted by the North Coast Regional Water Quality Control Board on June 28, 2001. Santa Rosa, CA. 124 p. Available online at: <http://www.waterboards.ca.gov/northcoast/programs/basinplan/083105-bp/basin-plan.pdf> Accessed 2006 12 February.

North Coast Regional Water Quality Control Board, Yurok Tribe, and Watercourse

Engineering. 2005. Klamath River Benthic Algae Monitoring Iron Gate Dam to Turwar 2004. Presented at the Klamath Basin Water Quality Monitoring Coordination Meeting on February 9, 2005 in Yreka, California. Available online at: <http://ncncr-isb.dfg.ca.gov/KFP/uploads/Benthic%20Algae%20Presentation.pdf> Accessed 2006 12 February.

PacifiCorp. 2003. Draft water resources technical report. Draft application for new license

for major project. PacifiCorp. Portland, Oregon. PacifiCorp. 2004. Final License Application for the Klamath River Hydroelectric Project

(FERC Project No. 2082). Portland, OR.


http://permanent.access.gpo.gov/waterusgsgov/water.usgs.gov/pubs/sir/2004/5047/pdf/sir2004.5047.pdf

http://permanent.access.gpo.gov/waterusgsgov/water.usgs.gov/pubs/sir/2004/5047/pdf/sir2004.5047.pdf

http://www.krisweb.com/biblio/klamath_nsa_nrc_2003.pdf

http://www.waterboards.ca.gov/northcoast/programs/basinplan/083105-bp/basin-plan.pdf

http://www.waterboards.ca.gov/northcoast/programs/basinplan/083105-bp/basin-plan.pdf

http://ncncr-isb.dfg.ca.gov/KFP/uploads/Benthic%20Algae%20Presentation.pdf

http://ncncr-isb.dfg.ca.gov/KFP/uploads/Benthic%20Algae%20Presentation.pdf

PacifiCorp. 2005a. Response to FERC AIR AR-1 Part (a), Technical Report, Conceptual Design and Preliminary Screening of Temperature Control Alternatives, Klamath Hydroelectric Project (FERC Project No. 2082). PacifiCorp. Portland, Oregon.

PacifiCorp, 2005b. Response to FERC AIR AR-1 Part (b), Technical Report, Evaluation of

the Preferred Design for Temperature and Dissolved Oxygen Control of Waters Discharged in the Klamath River from Iron Gate Dam, Klamath Hydroelectric Project (FERC Project No. 2082). PacifiCorp, Portland, Oregon.

PacifiCorp, 2005c. Response to FERC AIR AR-2, Final Technical Report, Anadromous Fish

Restoration, Klamath Hydroelectric Project (FERC Project No. 2082). PacifiCorp, Portland, Oregon.

PacifiCorp, 2005d. Response to FERC AIR GN-2, Status Report, Klamath River Water

Quality Modeling, Klamath Hydroelectric Project Study 1.3 (FERC Project No. 2082). PacifiCorp: Portland, Oregon. 131 pp.

Palmer, C.M., 1977, Algae and water pollution: Cincinnati, Ohio, U.S. Environmental

Protection Agency, EPA–600/9–77–036. Pascual, D.L. and L.P. Tedesco. 2003. Eagle Creek Reservoir: Responses to Algaecide

Treatment. Indiana University – Purdue University, Indianapolis, Department of Geology. Indianapolis, IN. 41pp. Available online at: <http://www.cees.iupui.edu/Research/Water_Resources/CIWRP/Publications/Reports/CEES-2004-02_2003-Algaecide-Study.pdf> Accessed 2006 12 February.

Pacific Fisheries Management Council (PFMC). 1994. Klamath River Fall Chinook Review

Team Report: An Assessment of the Status of the Fall Chinook Stock as Required Under the Salmon Fisheries Management Plan. PFMC, Portland, OR. 20 p. plus appendices.

Reiser, D. and T. Bjornn. 1979. Habitat Requirements of Anadromous Salmonids. In the

series Influence of Forest and Range Management on Anadromous Fish Habitat in Western North America. U.S. Forest Service Forest and Range Experiment Station, Portland, OR. Gen. Tech. Rep. PNW-96. 54 p.

Scott, C. 2005. Letter to FERC regarding Klamath Hydroelectric KHP (P-2082-027)

Response to AR-1(a) of FERC Additional Information Request dated February 17, 2005. PacifiCorp. Portland, OR.

Sjodin, A.L., W.M. Lewis Jr., and J.F. Saunders III. 1997. Denitrification as a component of

the nitrogen budget for a large plains river. Biogeochemistry 39: 327–342. Available online at: <http://cires.colorado.edu/limnology/pubs/Pub139.pdf> Accessed 2006 12 February.

Smith, Phil. Personal Communication. Director of Resighini Rancheria Environmental

Protection Agency, Klamath, California.


http://www.cees.iupui.edu/Research/Water_Resources/CIWRP/Publications/Reports/CEES-2004-02_2003-Algaecide-Study.pdf

http://www.cees.iupui.edu/Research/Water_Resources/CIWRP/Publications/Reports/CEES-2004-02_2003-Algaecide-Study.pdf

http://cires.colorado.edu/limnology/pubs/Pub139.pdf

Smith, V.H., and deNoyelles, F., 2001. A comparative water quality study of Cheney Reservoir, Kansas: Lawrence, University of Kansas Department of Civil and Environmental Engineering, final report to Wichita Water and Sewer Department, 56p.

Snyder, J. O. 1931. Salmon of the Klamath River, California. California Division of Fish and

Game, Fish Bulletin No. 34. Sacramento, CA. 121 pp. Available online at: <http://www.krisweb.com/biblio/klamath_cdfg_snyder_1931.pdf> Accessed 2006 12 February.

Stocking, R.W. and J.L. Bartholomew. 2004. Assessing links between water quality, river

health and Ceratomyxosis of salmonids in the Klamath River system. Oregon State University. Corvallis, Oregon. 5 pp.

Stocking, R.W. 2006. Presentation at the 2006 Klamath Fish Health Workshop on February

2, 2006, at Humboldt State University, Arcata, California. Stocking, R.W. Personal communication. Graduate student at Oregon State University,

Center for Fish Disease Research, Corvallis, Oregon. St. John, M. Personal communication. Water Resources Engineer at North Coast Regional

Water Quality Control Board, Santa Rosa, CA. Sullivan, K., D. J. Martin, R. D. Cardwell, J. E. Toll, and S. Duke. 2000. An analysis of the

effects of temperature on salmonids of the Pacific Northwest with implications for selecting temperature criteria. Sustainable Ecosystems Institute. Portland, OR. 192 pp. Available online at: <http://www.krisweb.com/biblio/gen_sei_sullivanetal_2000_tempfinal.pdf> Accessed 2006 12 February.

Tabachek, J.L., and Yurkowski, M., 1976, Isolation and identification of blue-green algae

producing muddy odor metabolites, geosmin and 2-methylisoborneol, in saline lakes in Manitoba: Journal of Fishery Research Board Canada, v. 33, p. 25–38.

Tencalla, F.G., D.R. Dietrich and C. Schlatter. 1994. Toxicity of Microcystis aeruginosa

peptide toxin to yearling rainbow trout (Oncorhynchus mykiss). Aquatic Toxicology, Vol. 30 (1994), pp 215-224

Tennant, D.L. 1976. Instream flow regimes for fish, wildlife, recreation and related

environmental resources. Fisheries 1(4): 6-10. Tetra Tech, Inc. 2004. Progress Report Development of Nutrient Criteria in California:

2003-2004. Prepared for US EPA Region IX. Tetra Tech, Lafayette, CA. Trihey and Associates. 1996. Instream Flow Requirements for Tribal Trust Species in the

Klamath River. Prepared on behalf of the Yurok Tribe. March. 43p. U.S. Bureau of Land Management (BLM). 2002. Instream Flow Analysis for the Bureau of

Land Management Federal Reserved Water Right, Claim Number 376, For the Klamath Wild and Scenic River in Oregon. May 2002. 92pp.


http://www.krisweb.com/biblio/klamath_cdfg_snyder_1931.pdf

http://www.krisweb.com/biblio/gen_sei_sullivanetal_2000_tempfinal.pdf

U.S. Bureau of Land Management (BLM). 2004. Bureau of Land Management’s comments on PacifiCorp’s “Spring Creek Water Quality Investigations” report for the Klamath hydroelectric project. Medford, Oregon. November, 2004. 20pp.

U.S. Environmental Protection Agency (US EPA). 1986. Quality criteria for water 1986:

EPA 440/5-86-001. Office of Water Regulations and Standards, Washington, DC. U.S. Environmental Protection Agency. 1999. 1999 update of Ambient water quality criteria

for ammonia. EPA 822/R-99-014. U.S. Environmental Protection Agency, Washington, D.C.

U.S. Environmental Protection Agency. 2000. Nutrient Criteria Technical Guidance Manual:

Rivers and Streams. Office of Water and Office of Science and Technology, Washington D.C. EPA-822-B-00-002.

U.S. Environmental Protection Agency. 2003. EPA Region 10 Guidance for Pacific

Northwest State and Tribal Temperature Water Quality Standards. EPA 910-B-03-002. Region 10 Office of Water, Seattle, WA.

Watershed Sciences, LLC. 2002. Aerial Surveys in the Klamath and Lost River Basins

Thermal Infrared and Color Videography. Prepared for the North Coast Regional Water Quality Control Board and Oregon Department of Environmental Quality. Watershed Sciences, Corvallis, Oregon. Available online at: <http://www.deq.state.or.us/WQ/TMDLs/KlamathBasin/FLIR/KlamathFLIR.pdf>

<http://www.deq.state.or.us/WQ/TMDLs/KlamathBasin/FLIR/KlamathFLIRAppxA.pdf> <http://www.deq.state.or.us/WQ/TMDLs/KlamathBasin/FLIR/KlamathFLIRAppxB.pdf>

Accessed 2006 12 February. Washington Dept. of Ecology (WDOE). 2002. Evaluating Criteria for the Protection of

Aquatic Life in Washington's Surface Water Quality Standards: Dissolved Oxygen. WDOE, Olympia, WA. 97 pp. Available online at: <http://www.ecy.wa.gov/pubs/0010071.pdf> Accessed 2005 1 April.

Wales, J.H. 1944. The Klamath River at Different Stages of Flow. California Department of

Fish and Game. Inland Fisheries Branch. Administrative Report 44-25, dated November 13, 1944. 13p.

Wells, S. A., R. Annear, and M. McKillip. 2004. Review of the Klamath River Model for the

Klamath Hydropower KHP FERC #2082. Prepared for the Bureau of Land Management and the Karuk Tribe. 130pp.

Welsh, H.W., Jr., Hodgson, G.R., Harvey, B.R., and Roche, M.F., 2001. Distribution of

juvenile coho salmon in relation to water temperatures in tributaries of the Mattole River, California: North American Journal of Fisheries of Management, v. 21, p. 464-470. Available online at: <http://www.krisweb.com/biblio/gen_usfs_welshetal_2001.pdf > Accessed 2006 12 February.


http://www.deq.state.or.us/WQ/TMDLs/KlamathBasin/FLIR/KlamathFLIR.pdf

http://www.deq.state.or.us/WQ/TMDLs/KlamathBasin/FLIR/KlamathFLIRAppxA.pdf

http://www.deq.state.or.us/WQ/TMDLs/KlamathBasin/FLIR/KlamathFLIRAppxB.pdf

http://www.ecy.wa.gov/pubs/0010071.pdf

http://www.krisweb.com/biblio/gen_usfs_welshetal_2001.pdf

Wiegland, C. and S. Pflugmacher. 2005. Ecotoxicological effects of selected cyanobacterial secondary metabolites, a short review. Toxicology and Pharmacology, Vol. 203, p201-218.

Wilkie, M.P and C.M. Wood. 1995. The adaptation of fish to extremely alkaline

environments. Comparative Biochemical Physiology. Vol. 113B, No. 4, p 665-673. Yoo R.S., W.W. Carmichael, R.C. Hoehn, S.E. Hrudey. 1995. Cyanobacterial (blue-green

algal) toxins: a resource guide. American Water Works Association. United States. Zambrano, F. and E. Canelo. 1995. Effects of Microcystin-LR on Partial Reactions of the

NA+-K+ Pump of the Gill of Carp (Cyprinus carpio). Toxicon, Vol. 34, No. 4, pp451-458.

Zedonis, P. 2005. Letter accompanying distribution of Arcata Fish and Wildlife Offices Water

Quality Monitoring Program 2004 DataSonde data. U.S. Fish and Wildlife Service, Arcata, CA. 1p.


Exhibit A Evidentiary Facts established about the JC Boyle Hydro Project Fish Passage

Facilities On the Klamath River

May 3, 2003 Downstream Passage Problems Existing Design Problems: The design parameters used for the construction of the existing downstream juvenile screens and bypass facilities are outdated and there is no practical or cost-effective means to reconstruct the facilities to meet current standards to allow for more efficient fish passage. Improving downstream fish passage with appropriate installation of screening facilities is an identified objective of the Klamath River Subbasin Fish Management Plan and is a goal of other agencies involved in the FERC re-licensing. Presently, each of the four entrances at the intake structure is equipped with Rex vertical traveling screens to prevent entrainment of fish into the power canal. The existing screens are 11’2” wide and 29’6” high at a low forebay of 3,788 ft. This screen height assumes 6 inches at the bottom of the screen is ineffective due to the normal seal arrangement. The gross approach area for each of the four screens is 329.4 square feet for a total gross area of 1,318 square feet. The resulting approach velocity with an intake flow is 2.3 fps, which, is almost six times the modern criteria of 0.4 fps. The existing screen bypass system, although consistent with the design one would normally expect for traveling band screens, does not meet modern design standards. The flow rate for the existing bypass is estimated at 20 cfs. High-pressure spray systems are supposed to keep the screens free of debris buildup. Fish screen housings were modified in 1988 to allow year-round operations, prior to that time, screens were removed during the winter period to avoid ice buildup. Metal screens were replaced in 1992 with 1/8 mesh, but debris occasionally damages the screens requiring time-consuming repair with no backup screens in place during repair. There is also no tailrace barrier at the powerhouse. Biological Studies and Results: • Beak consultants placed a fyke net in the fish ladder and fished once a week for a

24 hour period from April to mid-June and August through mid-October (City of Klamath Falls 1986). They estimated a downstream movement of 128, 246 juveniles.

• Researchers monitored downstream movement below JC Boyle Dam to measure possible recruitment from Spencer Creek but concluded that the low numbers were not adequate to maintain the population in the river between JC Boyle Dam and the state line. However, based on informal assessment of angler catches,


the trout populations appears to be sustaining a fishery with extremely conservative regulations of one trout per day, flies and lures only.

• Monthly reports documented fish salvages in the JC Boyle power canal of 133, 12 and 68 trout in July 1988, 1990 and 1991, respectively, when the project was shut down for annual maintenance. Fish ranged in size from 50-300mm. This was reported as “alarming as only a small percentage of the total volume of water in the canal was sampled, and that fish screens had been operating at JC Boyle since the last shutdown. The finding of fish in the canal seems to indicate the effectiveness of the Boyle dam fish screening devices are limited at best”. The July 1989 salvage report was missing.

• The May 1988 monthly report also reported sampling the attraction flow diffuser chamber at Boyle Dam with a backpack electroshocker, and 7 redband trout were from 142-337 mm.

• ODFW downstream trap captured 37,483 juvenile redband trout in Spencer Creek from October-November 1990, March through September 1991, October and November 1991 and March through May 1992. These numbers were not adjusted for trapping effort but show patterns of downstream timing and relative abundance. However, the downstream screw trap in the Klamath River immediately below JC Boyle fish bypass captured only 152 juveniles from April through December 1991, and late February through May 1992.

• PacifiCorp has documented all suckers and trout salvaged during project shutdown and maintenance operations since 1995. Since 1995, a total of 785 suckers and 919 redband trout have been salvaged during maintenance activities. Of the 785 suckers, 228 were federally listed species, of which shortnose and Lost River suckers comprised 24% and 5%, respectively. Of the 785 suckers, 533 were unidentified due to a small size of less than 6 inches, which makes species identification impossible.

Upstream Passage Problems Existing Design Problems: The design parameters used for the construction of the existing upstream adult fish ladder is outdated and there is no practical or cost-effective means to reconstruct the facilities to meet current standards to allow for more efficient fish passage. Improving upstream fish passage is an identified objective of the HOOPA FISHERIES’s Klamath River Subbasin Fish Management Plan and is a goal of other agencies involved in the FERC re-licensing. The JC Boyle dam has a pool and weir fish ladder with submerged orifices built during the 1957-1958 dam construction. The ladder is 569 feet long and the change in elevation between pool 1 and pool 57 is approximately 67 feet. Criteria at the time included 12 inch drops between pools and a vertical to horizontal slope of 1:8.5. Contemporary criteria for resident trout fishways are 6 to 9 inch drops between pools and minimum of 1:10 slope.


Flow in the ladder is estimated in September 2001 at 0.6 cfs through the 4 inch orifices and 20 cfs over the 6 foot wide weirs. The slope of the ladder is 1V:8.5H, which is steeper than both the current criteria for trout (1V:10H) and current criteria for suckers (1V:22H). With an approximate flow volume of 21 cfs, the turbulence factor for the typical pool is estimated at 6.8 ft-lb/s/ft3, which is 1.7 times the modern recommended value of less than 4.0 ft-lbs/s/ft3. • Attraction flow is limited to about 2% of the 10% annual exceedance flow,

whereas 5 to 10% is preferred for modern fishway design. The 10% annual exceedance flow for the flow duration curve is approximately 3400 cfs.

• Existing pool volume is generally too small for proper energy distribution. In general, pools are 6 feet wide by 8 feet long by 6 feet deep. Typical pool volumes for modern well-designed ladders are 8 foot wide by 10 foot long by 6 feet deep, allowing for fish to rest and stage for the next jump in the ladder.

• An automated gate with an auxiliary water supply system provides a total of about 80 cfs for attraction flow at the entrance, which is a discrepancy from the 2003 Ch2MHill report. It is uncertain, at the time of this review where the auxiliary water comes in – at the forebay or down the ladder. However, during observations by visiting biologists from USFWS, and during the 1988-91 ODFW study, ladder flows have ranged from nonexistent to raging whitewater.

• The existing entrance location to the fishway is difficult for fish to find during spill events and may be obscured by hydraulic problems and water quality differentials. Performing hydraulic study and/or site observations and basing the new entrance on the results of the study could improve the location of the entrance.

• There are also problems associated with different temperature and water quality between water from the bypass and ladder and water in the diversion reach. Flow issues need to reconcile releasing more water down the bypass reach to avoid water temperature and scent confusion to facilitate passage of adults in finding the entrance to the ladder.

• Design and construction of a new facility should include maximum flexibility to respond to future management decisions (e.g. anadromous fish reintroduction). This should include sorting and trap-and-haul facilities, adjustments to spillway and downstream facilities.

Biological Studies and Results: • A radio telemetry study is currently underway with 3 groups of 14 trout in each

group tagged at locations below JC Boyle dam. However, the study designs are not sufficient to establish the adequacy of the facility in regard to passing fish. Because of constraints in the study (e.g. Sample size of test fish) conclusions from these studies will not clearly establish the degree to which adult passage is compromised by the lack of adequate fish passage facilities at JC Boyle Dam.

• Estimates in 1960 and 1961 were 3,882 and 2,295 fish, respectively.


• Trapping efforts by Beak consultants in 1981 showed a small run of trout in the spring and the 1984 study showed a very small spring migration and a larger one in the fall.

• Beak consultants tagged 453 redband trout over 200 mm in the fall of 1988 downstream of the powerhouse (City of Klamath Falls 1989). ODFW monitored fish passage at the ladder in late 1988 through 1989. None of the tagged fish were observed in the fish ladder, and of those sampled in the ladder, 64% were less than 200 mm long.

• Research done from 1988-91 showed that by 1991 passage of redband trout over the dam had dropped to as low as 2% or the 1959 estimate (Hemmingsen et al. 1992). Numbers of fish were 507, 588, 412, and 70 in 1988, 1989, 1990, and 1991, respectively.

• Fluctuating flows through the fish ladder was frequently reported in the monthly HOOPA FISHERIES research reports. Since ladders are usually designed for an optimum hydraulic range for depth and velocity for migrating fish, passage is compromised by constantly changing flows in the ladder. The September 1989 flow fluctuation washed the trap to wash out twice. The June 1989 M.R. documented wild fluctuations of flow to the extreme when the ladder flow dropped to 0 cfs on one day.

• Research staff also noted numbers of fish captured in the JC Boyle Ladder trap increased sharply in days following periods of spill from the dam.

• There may be problems with diffusion pool of attractive water. The April 1988 monthly report noted that electroshocking samples regularly caught trout from 220-316 mm.

Planned Future Direction New, more effective downstream and upstream fish passage facilities need to be designed and constructed at JC Boyle Dam, with the above facts sufficiently establishing the biological rationale for replacement of the existing facilities. Design options will be developed in accordance with current standards and criteria of fish passage facilities and in consultation with the fish passage agencies, HOOPA FISHERIES, USFWS, and NMFS, and other interested members of the Klamath Fish Passage Work Group. The conceptual designs will be based on: 1) Maximize protection and safe and timely passage of all migratory fish species including native salmonids, suckers, lamprey including a design that will not preclude a no-jeopardy biological opinion for ESA listed fish, 2) Achieve fisheries management objectives (e.g. restore connectivity of migratory fish species), 3) Maximize productivity from upstream and downstream habitats, and 4) Ease of operations and maintenance and under a variety of hydraulic conditions.


Finally, the facts presented above in no manner constrain the Section 18 mandatory conditioning authority of the U.S. Fish and Wildlife Service and National Marine Fisheries Service, and Section 10j recommending authority of the Oregon Department of Fish and Wildlife. The facts will serve as substantial evidence to support decisions regarding replacement of the JC Boyle upstream and downstream fish passage facilities.


ATTACHMENT B

Lamprey Passage Recommendations for the

Klamath River

Prepared for: The Hoopa Valley Tribe

Prepared by:

Steward and Associates 120 Avenue A, Suite D

Snohomish, Washington 98290

February 24, 2006


Executive Summary The Klamath River Basin is home to a diverse assemblage of lamprey (Lampetra spp.), including at least seven species, featuring both resident and anadromous life-history types. Four of the known resident species are endemic to the basin. Historically, both resident and anadromous lamprey occupied the Upper Klamath Basin, but today the anadromous species are restricted to the lower river below Iron Gate Dam. Both resident and anadromous lamprey populations are adversely affected by Klamath River dams, including water-diversion impoundments as well as hydroelectric facilities. Reservoirs inundate countless kilometers of critical spawning and rearing habitat. The dams themselves act as physical barriers to upstream and downstream passage. Power-generation facilities cause high rates of direct mortality when fish pass through turbines, while also severely altering the natural flow regime in downstream areas. The dams and associated impoundments also alter other riverine processes, such as sediment transport and deposition, which affect lamprey survival and growth. PacifiCorp owns and operates seven hydroelectric facilities in the Klamath River Basin. The utility also operates two additional non-generating dams: the Link River Dam, which is associated with the East Side and West Side power canal developments, and the Keno Dam, located on the mainstem between the Link River and J.C. Boyle Dams. Limited fish passage is currently provided at a subset of the dams, primarily for the benefit of resident salmonids. PacifiCorp has applied to the Federal Energy Regulatory Commission for a new license to operate its hydroelectric project for another 30-50 year period. Although FERC has yet to specify terms for the new license, it is likely that provisions for fish passage will be included. It is important that fish passage measures provide for unobstructed upstream and downstream passage at each dam for all anadromous and resident fish species, including lamprey. Most fish ladders and juvenile bypass systems in the western United States have been designed primarily for salmon and trout. Rates of successful upstream passage are very high for salmonids at facilities that are properly designed and operated. Downstream passage success rates are generally much lower and highly variable, depending on the facility design, project operations and the species of interest. Unfortunately, upstream and downstream passage facilities designed for salmonids do not, in general, meet the needs of lamprey due to physiological, behavioral and life-history differences. However, research has shown that lamprey passage success can be substantially improved when conventional facilities are modified to account for some of these differences. In this report, following a brief description of the life history and distribution of Klamath Basin lamprey, we summarize research results regarding lamprey passage facility design and make specific recommendations for addressing the fish passage

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needs of lamprey at Klamath River dams. While we feel strongly that dam removal – coupled with habitat restoration – represents the best future scenario for lamprey recovery, every remaining dam should feature passage conditions that meet the unique life history and behavioral requirements of both anadromous and resident lamprey. Introduction On December 28, 2005, the Federal Energy Regulatory Commission filed a Notice of Application Ready for Environmental Analysis (REA) for the Klamath River Hydroelectric Project (FERC No. 2082) operated by PacifiCorp. FERC’s REA Notice triggered a 60-day period for providing comments, recommendations, terms and conditions, and prescriptions pertaining to the license application filed by PacifiCorp in February 2004. This report summarizes relevant knowledge regarding the distribution, life history and fish passage requirements for resident and anadromous lamprey known to exist in the Klamath River Basin. We then provide specific recommendations for new passage facilities and modifications to existing PacifiCorp hydroelectric projects to address the migratory requirements of lamprey. Species Information Lamprey Species in the Klamath Basin The Klamath River basin has a diverse assemblage of lamprey species of the genus Lampetra (Family: Petromyzontidae) including three non-endemic forms: the anadromous Pacific lamprey (L. tridentata), river lamprey (L. ayresi), and western brook lamprey (L. richardsoni); and four species that are endemic to the basin: the Klamath lamprey (L. similes), Miller Lake lamprey (L. minima), Pit-Klamath brook lamprey (L. lethophaga), and L. folletti. A fifth endemic – a non-anadromous form of the Pacific lamprey – completes its life cycle entirely in freshwater and probably warrants separate taxonomic status (Kostow 2002). Other lamprey species may be present as well; however, their presence and taxonomic status cannot be readily ascertained. Historically, the anadromous Pacific lamprey, L. tridentata, was the most abundant of the lamprey species present in the Klamath River basin, and has therefore received the most management and research attention (Hamilton et al. 2005). The comparatively large-bodied Pacific lamprey was listed as a “sensitive species” by the State of Oregon in 1993 due to the precipitous decline in its numbers observed over the preceding four decades (Weeks 1993, Close et al. 1995). The western brook lamprey is fairly abundant within the Klamath basin, but being smaller and less conspicuous than the Pacific lamprey, it is less commonly observed. The anadromous river lamprey, whose range extends from the Sacramento River

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northward to southeastern Alaska, are presumed to be limited in distribution to the lower Klamath River (Kostow 2002). The Miller Lake lamprey was declared extinct in the 1970s as a result of an intentional eradication program conducted by the state of Oregon (Bond and Kan 1973), but was rediscovered in two small drainages of the Upper Klamath Basin – the upper Williamson River and the upper Sycan River above Sycan Marsh (Lorion et al. 2000). The Pit-Klamath Brook Lamprey and the Klamath River Lamprey are closely related to the Pacific Lamprey. Both occur in the upper Klamath Basin above Klamath Falls. The Klamath River Lamprey is also found in the mainstem and tributaries downriver to Copco Dam No. 1. The L. folletti, as described by Vladykov and Knott (1976), occur in the Lost River and the Klamath Basin around lower Klamath Marsh near Klamath Falls. The L. folletti is relatively large with a more highly developed oral disc and dentition than other nonparasitic lamprey species. The current and historical presence of L. ferretti in the Klamath Basin is uncertain (Kostow 2002). Life History Although their cultural and ecological importance is increasingly recognized, and efforts to protect and restore their populations have intensified in recent years, many pivotal aspects of lamprey life history and biology remain enigmatic. Much of the information summarized below is derived from Kostow (2002), who provides a good overview of lamprey life history and habitat requirements. Lamprey eggs are non-buoyant and adhesive. Female lamprey deposit the eggs in shallow depressions (redds) dug by the males and females in sandy gravel along stream and river margins. The eggs incubate and hatch in 10 to 20 days depending on the water temperature, and perhaps varying by species. Newly hatched larvae, called ammocoetes, spend anywhere from one week to a month in the redd (Potter 1980), before drifting passively into backwater areas where they burrow into soft muddy substrates (Wydoski and Whitney 2003). Ammocoetes feed by filter feeding (Close et al. 2002). As they grow, over the course of four to six years, the larvae gradually move downstream, moving primarily at night and seeking coarser sand/silt substrates and deeper water (Pletcher 1963; Potter 1980). Older ammocoetes tend to accumulate in downriver areas. Growth rates vary seasonally and are influenced by water temperature and food supply. The most rapid increase in length occurs up until the time ammocoetes of most species reach about 10 cm in length. At this size lipid accumulation begins and the growth rate declines in preparation for the non-feeding period of metamorphism into an adult. As lamprey approach adulthood, they migrate to the ocean or to lakes where they live and feed for one to four years. Of the lamprey species found in the Klamath drainage, adults of the Pacific lamprey (including its non-anadromous form), the river lamprey, and the Miller Lake lamprey are parasitic; they attach themselves by their mouths to other fishes and feed on their

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tissues and body fluids. The adult western brook lamprey, Klamath lamprey, and Pit-Klamath brook lamprey are non-parasitic, feeding on live organisms and organic detritus. Anadromous lampreys return to fresh water in the fall, often migrating in large groups, and over-winter until spring when they spawn. Once they beginning their migration, lampreys do not feed. Courtship and spawning behavior of northwest lampreys has not been studied extensively. Pletcher (1963) described these behaviors for western brook lamprey and Beamish (1980) for Pacific Lamprey and river lamprey. All three species behave similarly; we therefore present a single general description below, following Pletcher (1963) and Beamish (1980). Spawning generally occurs in shallow riffles with sand and small gravel substrates. Spawning activity begins with courtship behaviors on spawning gravels. This includes nest-building and mutual displays. Solitary males, and perhaps some females, begin by preparing rudimentary nests. Courtship may be initiated by either gender by performing a “courtship glide”, where one lamprey glides along the body of a potential mate. A receptive mate will accompany the initiator to the rudimentary nest, which may be occupied by as many as a dozen individuals of both genders. It is believed that receptive females emit a chemical stimulus that attracts other lamprey, creating communal courtship (Pletcher 1963). Lampreys participating in communal courtship usually break into pairs or smaller groups and disperse to separate nests to spawn. Lampreys excavate their redds by carrying smaller rocks to the edge of the nest in their oral discs, pushing larger rocks, and moving finer substrates with rapid swimming motions. When the lampreys spawn, the male grasps the female by the back of the head and twists his tail around her. The female lays eggs in the rudimentary nest and undulates while the male performs most of the nest building. Paired spawning is most common, but polygamous and polyandrous group matings have been observed. Females deposit 100 to 500 eggs in each spawning bout. Between bouts, the female rests while the male enlarges the nest so as to not disturb previous egg deposits. This process repeats until all the eggs are deposited. It is generally believed that lamprey die soon after spawning due to the extreme physiological toll of spawning. Atrophying of the gut and filling of the body cavity with gonadal materials make it unlikely that individuals of either sex survive after spawning. Females have been described as living only a few hours to a week after spawning; males perhaps for a few weeks. However, several hundred apparently robust lamprey kelts were reported outmigrating on the Olympic Peninsula in Washington State and two marked individuals reportedly engaged in repeat spawning the following year (Michael 1980). ODFW staff and volunteers on the southern Oregon coast believe they have seen out-migration after spawning by some lamprey (Kostow 2002).

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Distribution and Current Status of Lamprey in Klamath River System Historical Distribution Native American accounts indicate that anadromous Pacific lamprey ascended to Klamath Lakes (Kroeber and Barrett 1960). However, some authors have suggested that reference to Pacific lamprey in the Upper Klamath Basin prior to dam construction may have been applied erroneously to resident taxa (Hamilton et al. 2005), which are known to occupy the upper portions of the basin. Gilbert (1898) reported observing a 26-cm “young” specimen in the upper basin; later studies indicate that the current lamprey found in Upper Klamath Lake of similar size are a distinct subspecies of L. tridentata (Kan 1975). Pacific lamprey were also reported in Fall Creek (Coots 1957). Lamprey are capable of migrating long distances, as evidenced by their extended migrations – in some cases exceeding 800 km – in the Columbia River and Snake River (Close et al. 1995). Historically, the upstream limits of Pacific lamprey distribution in the Columbia coincided with those of salmon (Simpson and Wallace 1978). Hamilton et al. (2005) concluded that anadromous Pacific lamprey would have historically migrated up the Klamath at least as far as Spencer Creek (RK 366) which enters the upper end of J.C. Boyle reservoir. This conclusion was based on several lines of evidence, including known lamprey distributions in other western coastal rivers, the presumptive overlap in the distribution of lamprey and anadromous salmonids, the absence of lamprey passage barriers in the mainstem Klamath Basin prior to dam construction, and the consistent composition of the fish community in the lower Klamath River upstream to Spencer Creek. Therefore it is reasonable to assume that the historical Pacific lamprey distribution extended to upstream limit of passage and habitat availability. Copco 1 Dam, completed in 1918, was the first man-made structure that physically prevented fish from migrating upstream in the mainstem Klamath River. Copco 2 Dam was built in 1925. Iron Gate Dam, the lowermost of the Klamath dams and the current upstream limit of anadromous fish passage, was constructed in 1962. Before these dams were built, fish freely accessed approximately 970 km of mainstem and tributary habitat upstream of Iron Gate Dam (Hamilton et al. 2005). Current Distribution Anadromous Pacific lamprey are widely distributed throughout the mainstem and primary tributaries of the lower Klamath River (PacifiCorp 2004). The presence of resident lamprey within the project area has been confirmed through electrofishing and other survey methods (PacifiCorp 2004). Lamprey have been found in both the East Side and West Side canal developments associated with Link River Dam, the 4.7-mile Keno reach downstream of Keno Dam, the 4.3-mile J.C. Boyle Dam bypass reach, and the 17.3-mile reach downstream of J.C. Boyle Dam. Little information is available regarding fish presence in the 0.3-mile reach between Copco No. 1 and

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Copco No. 2, but a mix of native and introduced fish species similar to those found in other reaches is presumed (PacifiCorp 2004). Lamprey were found in the J.C. Boyle, Copco and Iron Gate reservoirs by Oregon State University researchers in 1998 and 1999 (Desjardins and Markle, 1999). While detailed, species-specific distribution information is not readily available, resident species are known to currently reside in the upper basin above Upper Klamath Lake. Current Status Like the Columbia River and many other western rivers, hydroelectric dams on the Klamath River have contributed to declines in lamprey abundance by restricting or eliminating access to historical spawning areas. Historic lamprey abundance data in the Klamath Basin is largely non-existent, while the extremely limited data on current abundance are insufficient to ascertain historical trends (Kostow 2002). The majority of abundance data is anecdotal, or incidental catch records from salmonid monitoring where the methods and timing of efforts were not appropriate for effective sampling of lamprey. Despite the lack of quantitative data, it is apparent that lamprey numbers have declined in the Klamath River Basin (Larson and Bilchick 1998). The U. S. Fish and Wildlife Service was petitioned by several conservation organizations in January 2003 to list the Pacific lamprey, river lamprey, western brook lamprey, and Kern brook lamprey1 as threatened or endangered species under the Endangered Species Act (ESA). In late 2004, the agency declined to list any of the species, noting that the petition did not provide the required information to indicate that listing may be warranted. Lamprey Passage Upstream Adult Passage The majority of studies investigating the upstream passage of lamprey through hydroelectric projects have occurred on the Columbia River, where fish passage facilities at mainstem dams were designed primarily for the passage of adult anadromous salmonids (Mesa et al. 2003). Currently, lampreys must negotiate four hydroelectric dams to reach the confluence of the Columbia and Snake rivers, and up to five additional dams to reach spawning areas in the upper reaches of these rivers (Moser et al. 2002a). Adult lamprey are much less successful than salmon in navigating Columbia River fish ladders, considered to be among the best engineered fishways in the world. For example, fewer than 50% of the lamprey that arrive at the base of Bonneville Dam successfully ascend its fish ladder. Lamprey have difficulty passing John Day Dam (55%) and are only slightly more successful at passing The Dalles Dam (50-82%). Lamprey were reported to readily pass through high-velocity ladders, but had low passage efficiency through collection channels and transition areas with floor gratings 1 The Kern brook lamprey does not occur in the Klamath River system.

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that lack suitable attachment areas (Moser et al. 2002a). Lampreys lack swim bladders that allow them to maintain neutral buoyancy and therefore are required to constantly swim or adhere to a surface to maintain position (Mesa et al. 2003). Passage difficulties at dams experienced by upstream migrating lamprey may have lasting consequences. Pacific lamprey enter freshwater up to 12 months before spawning and may not eat during this time, and thus have finite energy reserves (Scott and Crossman 1973; Beamish 1980). Energy reserves may be significantly depleted by the effort required to negotiate fishways, potentially affecting reproductive success. Together, these factors exact a high energetic toll on lamprey; if their energy reserves are significantly depleted, lamprey are more susceptible to pre-spawning mortality. Factors Affecting Passage Success Studies on the swimming performance of sea lamprey (Beamish 1974; Bergstedt et al. 1981; Hansen 1980; Mcauley 1996) and Pacific lamprey (Moursund et al. 2003; Mesa et al. 2003; Close et al 2003) confirm that lamprey are poor swimmers compared to other teleosts. The anguilliform swimming motion used by lampreys is considerably less efficient than, for example, the carangiform (burst-and-glide) motion used by salmonids (Mesa et al. 2003). The swimming performance of fish is often described with respect to their critical swimming speed (Ucrit) and burst swimming speed. The critical swimming speed measures the fish’s swimming ability at maximum aerobic capacity (Hammer 1995). Swimming speeds that exceed the Ucrit can only be sustained for brief periods. Burst swimming speed is a measure of the speed at which fish can swim over short distances. When migrating upstream against a current, lamprey alternate between sustained and burst swimming to propel themselves upstream. In high velocity and turbulent flow, lamprey will often swim briefly at maximum speed, and then attach themselves by means of their suctorial disc to the bottom or side of the channel. After a period of rest, they will recommence swimming and re-attaching further upstream (Moser et al. 2002). Several studies have evaluated swimming speeds of Pacific lamprey. Moursund et al. (2003) reported burst swimming speeds for 125-170 mm long Pacific lamprey of 0.27 m/s to 1.0 m/s and sustained swimming speeds of 0.15 to 0.60 m/s. Mesa et al. (2003) reported that Pacific lamprey had mean Ucrit of approximately 0.85 m/s at 15°C, the average temperature of the lower Columbia River during the upstream migration of lampreys. Close et al. (2003) reported that Pacific lamprey can swim for up to an hour at 0.4 m/s, with durations ranging from 100 to 3,600 seconds. McCauley (1996) reported that sea lamprey were able to sustain swimming in water velocities of 1.5 m/s for up to 50 seconds, but could only swim for 2 to 3 seconds at 3 m/s. Beamish (1974) reported maximum sustained swimming speeds of 0.35 m/s at 15°C and 0.23 m/s at 2°C. Total distances traveled ranged from 13.8 to 21.3 m. Bergstedt et al. (1981) reported that at 1.4 m/s, lamprey could not sustain swimming

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for more than one minute. Hanson (1980) reported that in water temperatures below 15ºC few fish attempted to swim up a flume with velocities ranging from 1.5-4.0 m/s, but 17% (98 of 590) attempted to ascend the flume when temperatures ranged from 16-24ºC. Effects of Physical Conditions on Passage Success Lamprey are guided towards fishway entrances by hydraulic conditions (flow discharges, velocities and flow patterns) and other physical cues in the vicinity. The ability of lamprey to locate an entrance depends the existence of conditions that attract them and facilitate directional movements. Lamprey can be delayed in their upstream movements when they cannot locate fishway entrances due to turbulence and recirculation zones caused by turbine and spillway discharges. Lamprey typically swim near the streambed, taking advantage of lower velocities that occur in the shear region of the water-substrate interface. This may explain why adult Pacific lamprey were more likely to use orifice entrances located near the bottom of fishways than openings higher up in the water column (Moser et al. 2002b). Daigle et al. (2005) reported that Pacific lamprey typically used saltatory movements to approach and enter fishways. Lamprey would attempt to pass over the step leading into the fishway. If unsuccessful, they quickly attached to the bottom or sides of the channel and, after resting, tried again. Fishery managers have taken advantage of the poor leaping ability of sea lamprey by employing low-head dams (0.6-1.2 meter drop) to prevent upstream movements and subsequent spawning in tributaries to the Great Lakes (McCauley 1996; Porto et al. 1999) and Lake Champlain (Marsden et al 2003). Daigle et al. (2005) reported that Pacific lamprey had difficulty negotiating a vertical step in an experimental fishway. In this case, passage rates of Pacific lamprey decreased from 69% to 49% when a 0.2-meter high step was added downstream of an orifice in an experimental fishway. It is not uncommon for adult lamprey to fail to gain entry or, if they do succeed, to successfully pass from one compartment or pool to the next in a fish ladder (Close et al. 1995). To enter and move upstream through a fishway, adult lamprey must either leap over a weir or swim around a baffle that serves as a hydraulic control. Weir crests and the vertical slots created by baffles are high velocity regions. Lamprey have difficulty negotiating sharp-angled corners in such situations (Moser et al. 2002b). Round corners reduce shear velocities and provide better purchase, thereby facilitating passage. Daigle et al. (2005) and (Moser et al. 2002b) reported higher passage success with rounded corners than squared corners in laboratory testing. The ability to find attachment sites is key to lamprey passage through areas of high velocity in fishways (Moser et al. 2002b). Studies indicate that metal grating on the floor of fishways can result in poor fish passage efficiency (Daigle et al. 2005; Moser et al 2002; Moser et al 2003). The authors found that diffuse grating placed just upstream of an orifice increased the time it took for lamprey to navigate an experimental fishway. Therefore, it is critical that adequate attachment surfaces are

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available in high velocity areas in order for lamprey passage to be successful in fishways. Although there is limited information on the relationship between water temperature and lamprey passage at hydroelectric projects, studies suggest that water temperature strongly influences the migration behavior of lampreys (Malmquist 1980; Bayer et al. 2000, Almeida et al. 2002). Changes in temperature affect both juvenile lamprey outmigration and the timing of spawning migrations by adults. At Bonneville Dam and The Dalles Dam on the Columbia River, adult lamprey moved upstream through the tailrace and fishways with increased water temperature (Ocker et al. 2001). However, significantly fewer lamprey successfully passed Bonneville Dam when water temperatures exceeded 19.5, indicating that exceedingly high temperature may be a barrier to lamprey movement (Ocker et al. 2001). Low water temperatures may also affect the rate of adult lamprey migration. Bayer et al. (2000) reported increased holding behavior (i.e., temporary halting of migration) with decreased water temperature, daylight, and discharge in the John Day River. Downstream passage Hydroelectric projects often alter the movements of juvenile lamprey that are migrating downstream, and in many instances cause their injury or death. Juvenile lamprey suffer lower injury and mortality rates due to turbine passage than do juvenile salmonids. However, juvenile lamprey are more apt to be entrained in turbines because they tend to stay low in the water column and are less able to overcome the high water velocities associated with turbine intakes (Long 1968; C. G. Reyes, R. A. Moursund, M. D. Bleich 2006). Screens are frequently placed in front of turbine intakes to intercept downstream migrating fish and divert them away from turbines and into collection facilities. For example, turbine intakes on the mainstem Columbia River Dams are equipped with extended-length submerged bar screens that guide fish into gatewells, from which they enter the collection channel via submerged orifices. Fish entrained in the collection channel, which runs laterally along the powerhouse, are either released back into the river or shunted into a fish holding facility at the base of the dam. Screens pose a hazard to juvenile lamprey that encounter them. Water velocities near the screen face are generally in excess of the swimming capability of juvenile lamprey, and as a result they are often pinned and unable to free themselves. Investigators have reported large numbers of juvenile lamprey impinged on bar screens at The Dalles and McNary dams (Hatch and Parker 1998). In laboratory experiments, Moursund et al. (2000) reported that 70% and 97% of test fish became impinged on bar screens when exposed to a 0.5 m/sec velocity for 1 minute and 12 hours, respectively. A significant percentage of juvenile lamprey also became stuck when velocities ≥0.3 m/s over 12-hour exposure periods. The authors reported that juvenile lamprey have difficulty extricating themselves from screens at velocities ≥0.5 m/s.

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Passage considerations summary Several investigators have noted that the upstream movements of adult lamprey in the Columbia River system are impeded by hydroelectric dams and by the physical conditions associated with fish passage facilities (Haro and Kynard 1997; Mesa et al. 2003; Moser et al. 2002a; Moser et al. 2002b; Daigle et al. 2005). Successful attempts by adult lamprey to pass upstream via fish ladders have nevertheless been reported (Moser et al. 2002b). Although lampreys are capable of ascending fishways under certain circumstances, available evidence suggests that passage success rates are low. Assuming that the passage success rates reported by Moser et al. (2002a) for several lower Columbia River dams are representative, between 18% and 50% of the lamprey can be expected to fail in their attempt to pass a typical fishway. If four dams must be navigated, anywhere from 87% to 45% of the lamprey arriving at the first dam will be lost before the uppermost dam is passed. It is likely adult lamprey, even if they are successful, are indirectly affected by the delay and increased expenditure of energy required to negotiating fishways. Migratory stress and delays may disrupt important physiological and behavioral processes necessary for sexual maturation and successful reproduction (Mesa et al. 2003). Adult lamprey have difficulty negotiating the high velocities and sharp-angles associated with weir crests and baffles that are common in fishways. They also have difficulty ascending collection channels and transition areas with floor gratings that lack suitable attachment areas (Moser et al. 2002a). Much of the information relating to the swimming performance of lampreys pertains to the better known and larger bodied anadromous species. Adults of smaller species of lamprey that occur in the Klamath basin, especially non-anadromous forms, are likely to have substantially lower swimming capabilities. Therefore, design criteria for upstream passage facilities should take into account the specific requirements of these smaller lamprey. Due to similarities in morphology, habitat use and life history, the juvenile form (ammocoete) of various lamprey species exhibit similar behaviors and swimming capabilities. After residing in their natal tributaries for a number of years, juvenile lamprey migrate downstream to oceans and lakes where they metamorphose and take up residence as adults. Hydroelectric projects can delay juvenile migrants, and in many instances, cause significant injury or death. Juvenile lamprey are apt to be pass through turbines due to their tendency to migrate close to the bottom and because they are weak swimmers. They are especially vulnerable to impingement on turbine intake screens intended to divert downstream migrants away from turbines and into fish collection facilities. Most juvenile lamprey that become impinged on screens are unable to escape, and therefore die.

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Current Klamath River fish passage facilities Iron Gate Dam, the lowermost of the Klamath dams, lacks fish passage facilities and therefore constitutes a complete barrier to upstream migrating adult lamprey. All species of anadromous fish in the Klamath are denied access to areas above this point. However, some of the dams upstream of Iron Gate Dam are equipped with upstream and downstream passage facilities. These facilities are primarily intended to facilitate the migration of resident salmonids, though they are used to some extent by other species, such as sucker and lamprey. Detailed descriptions of each facility are provided elsewhere (PacifiCorp 2004; FishPro 2000). Table 2 summarizes the existing facilities at each dam.

Table 1. Existing fish passage at Klamath River project facilities.

Link River East/West Side Keno J.C. Boyle Copco 1 & 2 Iron Gate Fall Crk

Upstream Yes No Yes Yes No No No

Downstream No No See (1) Yes No No No (1) Downstream passage occurs at Keno Dam via spill and flow through the ladder.

Upstream passage facilities The Link River Dam - which is directly associated with the East Side and West Side power canals - has an existing fish ladder, as does Keno Dam. The original ladder at the Link River Dam does not meet applicable agency standards for passage of resident suckers – a key species of concern in the Upper Klamath basin. The USBR has recently constructed a new ladder at the dam that meets applicable criteria and provides potential upstream access to suckers, salmonids and presumably lamprey. A key feature of a sucker-focused ladder compared to a resident salmonid ladder is the more gentle slope of the structure. While salmonid passage facilities are generally constructed with a 1:10 slope (i.e., 1 meter of rise for every 10 meters of horizontal distance), sucker facilities must meet a standard of 1:22. Keno Dam included a fish ladder in its original construction. While the slope of the Keno ladder is suitable for salmonids (approximately 1:10.5), it does not meet sucker requirements. Furthermore, many other modifications are also required before the dam will meet current standards. Similarly, though the ladder at J.C. Boyle met passage criteria required at the time it was constructed, it falls short of several current criteria for resident salmonids, such as the allowable vertical drop from pool-to-pool during certain flow conditions. Serious concerns have also been expressed regarding the efficacy of the facility during spill events at the dam due to inadequate attraction flow at the ladder entrance. The 1:8.5 slope may be nearly adequate for salmonids, but is clearly too steep for suckers. Copco No.1 and No.2 do not have adult (or juvenile) passage facilities of any kind. The Iron Gate Dam has two, short adult-collection ladders for capturing hatchery broodstock. One is located at the base of the dam, while the second ladder is

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located just downstream at the hatchery. Reportedly, the hatchery ladder – which utilizes hatchery effluent flow as attraction flow - tends to capture a larger share of adult migrants. While these ladders do not currently provide passage, they could, in theory, be used as upstream-migrant collection points for tram, lock, lift or trap-and-haul passage facilities in the future. This issue is discussed in greater detail, below. The Fall Creek dam does not have upstream passage facilities. The dam itself is located upstream of an impassable water fall. The bypassed portion of the creek (below the dam) is known to contain resident species that are currently unable to pass the diversion dam and return to upper portions of the creek. Downstream facilities The East Side and West Side facilities do not have any downstream passage facilities in place. Fish may pass through the project turbines or via spill, but mortality rates are typically quite high for turbine passage. Spill passage survival, on the other hand, can be very high, depending on the configuration of the spillway. However, spill is generally infrequent at facilities that are geared for power production. As indicated in Table 2, fish are able to pass downstream past the Keno facility via spill and, to a lesser degree, via flow in the fish ladder. The dam has no power generation facilities and operates primarily to regulate water levels in Keno reservoir. During certain flow conditions, resource agencies have expressed concern that the spillway does not function well as a passage facility and requires modifications to be suitable for resident or anadromous species, but bypass screens or surface collectors (e.g., gulpers) are not perceived necessary at this facility. The J.C. Boyle dam has an intake screen and bypass system for juvenile passage. The screen does not meet current standards in several areas, such as an excessive approach velocity of 2.3 feet-per-second (fps), nearly six times the recommended velocity for a resident trout passage facility (0.4 fps). Also, screen mesh size does not meet standards, and the lack of back-up screens means that turbine intakes are not screened during maintenance activities (PacifiCorp 2004), forcing fish to pass through turbines. The Fall Creek diversion dam does not currently have passage facilities or exclusion devices to prevent juvenile fish entrainment. PacifiCorp argues that the need for downstream passage protection facilities for resident fish is “debatable”, and that turbine entrainment and subsequent rates of mortality do not pose a significant adverse risk to resident fish species in the Klamath (PacifiCorp 2004, Sec. 7.12.2.3). They base this argument on the following lines of reasoning: the reservoirs are dominated by introduced, rather than native species; entrainment mortality rates themselves are presumably quite low, particularly for the most likely sizes of fish entrained; and that entrainment reduces density-dependent effects on reservoir populations, thereby resulting in higher survival for remaining

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fish. While we find these arguments misplaced for all resident species, they are particularly erroneous in the case of lamprey for the following reasons:

• Lamprey are a native species. Even if the majority of entrained fish are non-native, and even if it is deemed appropriate to sacrifice non-native species to turbine entrainment, this does not in any way reduce the turbine-related mortality of native lamprey and other native species.

• PacifiCorp cites evidence from other projects that small fish tend to survive turbine passage at a higher rate than large fish. This may be true, but PacifiCorp assumes that the average size for a fish likely to pass through turbines on the Klamath is 50-75 mm with a modest mortality rate of 10%. However, depending on age, lamprey may be substantially larger than this conservative estimate. Many measure 100 mm after just one year of growth. By PacifiCorp’s own estimates, mortality rates may be as high as 35-40% for fish >150 mm at the J.C. Boyle project due to the high peripheral runner velocity in those particular turbines (PacifiCorp 2004).

• • To make the argument that turbine entrainment and mortality are a benefit to

the remaining population due to a reduction in density-dependent effects, PacifiCorp would first have to provide compelling evidence that populations of the species of concern are at a level where density-dependent effects are occurring. This is clearly not the case for lamprey which have been petitioned for listing under the Endangered Species Act in the Klamath basin. We find it doubtful that this would be the case for any other native species in the project area.

• Passage recommendations for lamprey General recommendations The best option for restoring resident and anadromous lamprey populations – as well as resident and anadromous salmonids – is dam removal. While removal of all dams on the river is clearly the best long-term option from a fish recovery perspective, politically it is unlikely to occur. However, short of complete removal, the selective removal of a subset of dams, coupled with ecological restoration, would likely provide the greatest benefits for the largest number of species. Inundated mainstem habitat between Iron Gate Dam and the Link River Dam totals approximately 38 miles, in addition to many more miles of the inundated lower reaches of tributaries, such as Spencer Creek, Jenny Creek and Fall Creek. These areas were likely very important components of lamprey habitat prior to the construction of the projects. Lamprey spawning and early-rearing habitat in the current configuration is very limited. Those reaches of the mainstem Klamath that are not inundated (e.g., reaches below Keno, J.C. Boyle, Copco No. 2) are nevertheless profoundly affected by the projects. These reaches may provide some lamprey spawning habitat, although the lack of gravel and sand input reduces suitability (see life history section, above). Lower-energy backwater areas utilized by juveniles for prolonged rearing

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periods are largely absent, and the flow variability imposed by power-peaking operations likely strands countless juvenile fish and dewaters redds. For those dams that are not removed, substantial improvements to current passage facilities and the construction of additional facilities are required to ensure adequate protection and passage for anadromous and resident species of lamprey. While specific lamprey-based criteria have not been developed by management agencies, passage criteria for other sensitive species or salmonid lifestages provide useful guidance. For example, the National Marine Fisheries Service’s juvenile screen criteria (NMFS 1995) make a distinction between fry-size and fingerling-size salmonids. Passage criteria for fry-sized fish reflect their higher level of vulnerability to injury, death and delay. In general, both upstream and downstream facilities must emphasize volitional passage rather than trap-and-haul operations. Specifically, by the term ‘volitional’, we refer to facilities that operate effectively during all flow conditions (with the possible exception of extreme high flows), allow fish to migrate at their own pace (i.e., minimal delay), minimize handling and sorting, do not involve transportation by vehicles, and allow fish to have access to all portions of the basin, including all areas between dams. All such facilities must also provide safe, timely and effective passage for all species. In the downstream direction, we consider full criteria intake screens coupled with bypass systems – modified as appropriate to meet lamprey needs - to match this description, as well as safely designed spill passage that operates year-round (e.g., modified spill facility at Keno). Bypass screen mesh size should be ≤ 3.175 mm (1/8 in.) to protect juvenile lamprey from impingement. NMFS juvenile screening guidelines for fry-size (up to 60 mm) salmonids should suffice as the required mesh size is < 2.38 mm (0.0938 in). Similarly, NMFS’ approach-velocity criteria for salmonid fry (0.12 m/s, or 0.4 ft/s) should also be adequately protective of lamprey. We are not aware of any evidence to suggest that experimental surface collectors (i.e., gulpers) are effective in collecting lamprey, nor are they as effective in passing salmonids as full screens. For this reason, we do not recommend the use of such facilities in the Klamath. In the upstream direction, ladders are the facility of choice, assuming that they are modified to address lamprey needs while also meeting salmonid and sucker criteria. Specific modifications are described below. Lock, tram, and lift type systems – while generally inferior to ladders - may be appropriate at some facilities. For example, as suckers are known to have trouble scaling past high-head dams, a well designed alternate may be feasible. Such facilities must reduce delay by operating at a high-frequency, ensure appropriate temperature control, while also meeting the other requirements for volitional passage described above. Ladder entrances to such facilities must meet the standards for salmonids and suckers, as modified for lamprey.

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Volitional passage is particularly important for lamprey due to the inherent difficulties in sorting and identifying specific species, especially at the juvenile stage. If trap-and-haul were used to transport juveniles around all the dams or a subset of dams, resident fish would likely be transported erroneously to the lower Klamath River below Iron Gate Dam. While they may survive or even thrive in downstream areas, the unintended effect would be the further erosion of the local populations in the upper basin which are already in perilous condition. The remainder of our recommendations focus on specific needs at each of the project facilities. These considerations must be incorporated into the Licensee’s designs required by recommendations 3 (upstream fish passage) and 4 (downstream fish passage), above. Link River, East Side and West Side If the East Side and West Side facilities are decommissioned as proposed in the current application, the following recommendations regarding downstream passage will be irrelevant. In this scenario, improvements to downstream passage via spill would be the responsibility of the USBR rather than PacifiCorp. However, if the facilities are retained, or if decommissioning is delayed by several years, then passage facilities should be constructed as described, below. 1. Install full criteria intake screens with bypass facilities for downstream passage

in East Side and West Side Canals Prior to applying for project decommissioning at the East Side and West Side facilities, PacifiCorp developed conceptual designs for both traditional (i.e., full criteria) and high-velocity screens as possible solutions to juvenile passage at the East Side and West Side facilities (PacifiCorp 2004). The primary advantage of high-velocity screens is their reduced cost. The primary disadvantage is the reduced screen size (not mesh size) – roughly 25% of a conventional screen – which leads to a four-fold increase in approach velocity. As described above, lamprey are particularly vulnerable to injury and impingement in high-velocity facilities. The recommended approach velocity for resident trout and salmon fry of 0.12 m/sec (0.4 ft/s) is likely a maximum velocity for adequate protection of lamprey. Screen mesh size should be ≤ 3.175 mm (1/8 in) to reduce impingement.

2. Conduct studies to test the efficacy of the new Link River ladder (USBR project) for passing lamprey.

The new USBR upstream passage facility is reportedly designed to meet the needs of resident trout and suckers. Studies to evaluate passage by adult lamprey of different sizes and species should be conducted in an effort to inform design of other facilities in the basin. The lower velocities and gradual slopes intended for the benefit of suckers will likely benefit lamprey as well. However, other factors, such as the presence/absence of attachment surfaces, orifice placement, or the presence/absence of sharp turns may affect suitability for lamprey.

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Keno Dam If the Keno facility is removed from the purview of the FERC, it may be difficult to compel PacifiCorp or a future owner to modify the facilities to address fish passage needs. The following actions should be required of PacifiCorp as a condition of removing the project from the FERC license. 1. Modify spillway to improve downstream passage during all flows. ODFW has expressed concerns about the inadequate width of the spillway opening at low flows. While spill passage is a desirable mode of downstream passage at a low-head facility, the facility and operations should be optimized to provide safe, timely and effective passage at all flows. 2. Construct new ladder to meet the needs of lamprey, suckers, and both

anadromous and resident salmonids. The Keno ladder should be replaced with a ladder that meets the passage needs of all key species. The current slope is inappropriate for suckers, and ODFW has expressed concerns about the ability of the ladder to produce sufficient attraction flow, particularly when the dam is spilling. To meet lamprey needs, the ladder should feature attachment surfaces (particularly just above orifices, low velocities, and rounded (rather than 90 deg.) corners wherever possible. The new Link River ladder can potentially be used as a test facility for various ladder modification options. J.C. Boyle Dam 1. Install full criteria intake screens with bypass facilities for downstream passage

at the J.C. Boyle Dam. In the supporting documentation for PacifiCorp’s license application, both traditional (i.e., full criteria) and high-velocity screens are presented as possible solutions to juvenile passage at the J.C. Boyle facility. The primary advantage of high-velocity screens is their reduced cost. The primary disadvantage is the reduced screen size – roughly 25% of a conventional screen – which leads to a four-fold increase in approach velocity. As described above, lamprey are particularly vulnerable to injury and impingement in high-velocity facilities. The recommended approach velocity for resident trout of 0.4 ft/s is likely a maximum velocity for adequate protection of lamprey. 2 Construct new ladder to meet the needs of lamprey, suckers, and both anadromous and resident salmonids. The J.C. Boyle ladder should be replaced with a ladder that meets the passage needs of all key species. The current slope is inappropriate for suckers, and ODFW has expressed concerns about excessively high temperatures in the ladder which are substantially higher than temperatures in the bypass reach just downstream. To meet lamprey needs, the ladder should feature attachment surfaces (particularly just above orifices), low velocities, and rounded (rather than 90 deg.) corners wherever possible.

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Copco No. 1 and Copco No. 2The configuration of the Copco dams presents particular challenges and trade-offs for purposes of fish passage planning, particularly in the upstream direction. The two dams are separated by a 0.3 mile canyon reach that provides limited habitat value. While access to all potential habitat is preferred, it must be weighed against the inevitable fish losses and delays associated with each step of the passage process. PacifiCorp has suggested that an upstream passage facility at Copco No. 2 could be constructed so as to transport fish from the base of the dam to the forebay of Copco No.1. This option should be given serious consideration if both Copco dams are to remain in place. 1. Install full criteria intake screens for downstream passage at Copco No. 1 and

Copco No.2. In the license application, both traditional (i.e., full criteria) and high-velocity screens are presented as possible solutions to juvenile passage at the Copco dams. For reasons described above, we recommend against the selection of high-velocity screens or Gulpers in lieu of conventional full-criteria screens. The recommended approach velocity for resident trout of 0.4 ft/s is likely a maximum velocity for adequate protection of lamprey. 2. At Copco No. 1, bypass screened fish to Copco No. 2 tailwater. The most difficult element of fish passage is the safe and effective capture of juvenile migrants. Given the very short length of the accessible reach and the ensuing difficulty of subsequent capture at Copco No. 2, we recommend bypassing screened migrants past the lower dam. 3. Construct aerial tramway with lock or ladder to transport adults from Copco

No. 2 tailwater to Copco No. 1 forebay. The height of Copco No. 2 does not preclude the construction of a conventional ladder. However, while ladders are generally preferable to trams, the height of Copco No.1 likely necessitates an alternative to a conventional fishway. Given the short length of the intervening reach, it may be preferable to tram fish over both dams in the upstream direction. Any tram facility must ensure proper temperature control during all seasons and flow conditions. Such a facility would likely require a short ladder at its base. Such a ladder must incorporate the design characteristics described above to provide safe, timely and effective passage for lamprey, while also meeting the criteria for suckers and salmonids. Iron Gate Dam Due to the height of Iron Gate Dam, the California Department of Fish and Game, the U.S. Fish and Wildlife Service and NOAA Fisheries have expressed doubt about the likely feasibility of a conventional ladder as a passage option at Iron Gate. The absence of similar high-head projects with successful ladders for anadromous salmonids and lamprey is a key factor influencing agency recommendations. Given the modest passage success rates for lamprey at passage facilities on the Columbia

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River, consideration of a tram/lock option may be warranted as a the next-best alternative. We strongly recommend against a trap-and-haul mode of upstream transport. 1. Install full criteria intake screens with bypass facilities for downstream passage

at the Iron Gate Dam. In PacifiCorp’s license application, both traditional (i.e., full criteria) and high-velocity screens are presented as possible solutions to juvenile passage at the Iron Gate facility. The primary advantage of high-velocity screens is their reduced cost. The primary disadvantage is the reduced screen size – roughly 25% of a conventional screen – which leads to a four-fold increase in approach velocity. As described above, lamprey are particularly vulnerable to injury and impingement in high-velocity facilities. The recommended approach velocity for resident trout of 0.4 ft/s is likely a maximum velocity for adequate protection of lamprey. 2 Construct or modify existing fish-collection ladders to serve as entrances for tram/lock passage system. Existing ladders must be modified to meet the passage needs of anadromous Pacific lamprey in particular, as described above for other facilities. 3. If existing hatchery ladder is to be used for fish collection, replace current

water source. The attraction water for the current hatchery ladder is supplied by effluent from the hatchery. While this can be effective for capturing hatchery fish, attraction of reintroduced anadromous salmonids and native lamprey should be avoided. These fish should be encouraged to develop natural homing instincts for the upper watershed. Moreover, as fish will be passed into the upper basin, transmission of hatchery-origin diseases is a serious concern. Fall Creek Dam 1. Install screens with bypass facilities in the diversion power canal, bypassing

fish into Fall Creek below the diversion dam. Currently, when resident fish get entrained into the diversion canal, they are forced to either persist in the canal itself or pass through the turbines into Iron Gate reservoir, unable to return to Fall Creek. Low-velocity, small-mesh screen should be used to reduce impingement and other physical harm to resident fish, including lamprey. 2. Construct fish ladder to allow fish to pass from lower Fall Creek into upper Fall

Creek. This low-head diversion dam is easily scaled by resident fish via a properly designed ladder. Physical design considerations for lamprey listed above should be included.

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References Almeida, P. R., B. R. Quintella, and N. M. Dias. 2002. Movement of

radio-tagged anadromous sea lamprey during the spawning migration in the River Mondego (Portugal). Hydrobiologia 483:1-8.

Bayer, Jennifer, T. Robinson, James Seelye. 2000. Upstream Migration of Pacific Lampreys in the John Day River; Behavior, Timing, and Habitat Use. 2000 Technical Report, Project No. 200005200, 46 electronic pages, BPA Report DOE/BP-26080-1.

Beamish, F. W. H. 1974. Swimming performance of adult sea lamprey, Petromyzon marinus, in relation to weight and temperature. Transactions of the American Fisheries Society 103:355-358.

Beamish, F. W. H. 1980. Adult biology of the river lamprey (Lampetra ayresi) and the Pacific lamprey (Lampetra tridentate) from the Pacific Coast of Canada. Canadian Journal of Fisheries and Aquatic Sciences 37:906-1923

Bergstedt, R. A., D. V. Rottiers, and N. R. Foster. 1981. Laboratory determination of maximum swimming speed of migrating sea lampreys: a feasibility study. U. S. Fish and Wildlife Service Administration Report No. 81-3.

Clay, C. H., 1995. Design of fishways and other fish facilities, 2nd edition. CRC Press,Inc., Boca Raton, Florida.

Close, D. A. M. S. Fitzpatrick, H. Li, B. Barker, D. Hatch, and G. James. 1995. Status report of the Pacific lamprey (Lampetra tridentata) in the Columbia River Basin. U.S. Department of Energy, Bonneville Power Administration, Environment, Fish, and Wildlife, Portland, OR.

Close, D. A., M. S. Fitzpatrick, and H. W. Li. 2002. The ecological and cultural importance of a species at risk of extinction, Pacific Lamprey. Fisheries 27: 19-25.

Coots, M. 1957. The spawning efficiency of king salmon (Onchorhynchus tshawytcha) in Fall Creek, Siskiyou County. 1954-55 Investigations Inland Fisheries, California Department of Fish and Game, Inland Fisheries Branch, Administrative Report 57-1. Redding.

Daigle, W. R., C. A. Peery, S. R. Lee, and D.F. Markle. L. Moser. 2005. Evaluation of adult lamprey passage and behavior in an experimental fishway at Bonneville Dam. Prepared for U.S. Army Corps of Engineers, Portland District, and Bonneville Power Administration, Portland, Oregon.

Desjardins, M.Daigle, W. R., C. A. Peery, S. R. Lee, and D.F. Markle. 1999. Distribution and Biology of Suckers in Lower Klamath Reservoirs. 1999

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Final Report. Submitted to PacifiCorp by Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR.M. L. Moser. 2005. Evaluation of adult lamprey passage and behavior in an experimental fishway at Bonneville Dam. Prepared for U.S. Army Corps of Engineers, Portland District, and Bonneville Power Administration, Portland, Oregon.

FishPro. 2000. Fish Passage Conditions in the Upper Klamath River. Prepared for the Karuk Tribe and PacifCorp.

Gilbert, C. H. 1898. The fishes of the Klamath Basin. Bulletin of the United States Fish Commission 17.

Hamilton, J. B., G. L. Curtis, S. M. Snedaker, and D. K. White. Distribution of andadromous fishes in the upper Klamath River watershed prior to hydropower dams – a synthesis of the historical evidence. Fisheries 30(4): 10-20.

Hammer, C. 1995. Fatigue and exercise tests with fish. Comparative Biochemistry and Physiology 112A:1-20.

Hanson, L. H. 1980. Study to determine the burst swimming speed of spawing-run sea lampreys (Petromyzon marinus). U.S. Fish and Wildlife Service, Research Completion Report, Millersburg, Michigan.

Hanson, L. H. 1980. Study to determine the burst swimming speed of spawning-run sea lampreys (Petromyzon marinus). U. S. Fish and Wildlife Service, Research Completion Report, Millersburg, Michigan.

Haro, A. and B. Kynard. 1997. Video evaluation of passage efficiency of American shad and sea lamprey in a modified Ice Harbor fishway. North American Journal of Fisheries Management 17:981-987.

Hatch D, and B Parker. 1998. Lamprey Research and Restoration Project. 1996 Annual Report: Part (B) Abundance Monitoring for Columbia and Snake Rivers. Prepared by Columbia River Intertribal Fish Commission, Portland, Oregon, for Bonneville Power Administration, Portland, Oregon.

Kan, T. T. 1975. Systematics, variation, distribution, and biology of lampreys in the genus Lampetra in Oregon. Doctoral dissertation, Oregon State University, Corvallis.

Kostow, K. 2002. Oregon lampreys: natural history, status and analysis of management issues. Fish Division, Oregon Dept. Fish and Wildlife.

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Larson, Z. S. and M. R. Belchick. 1998. A preliminary status review of eulachon and Pacific lamprey in the Klamath River Basin. Yurok Tribal Fisheries Program, Klamath, CA.

Long CW. 1968. “Diurnal movement and vertical distribution of juvenile

anadromous fish in turbine intakes.” Fisheries Bulletin 66:599-609.

Lorion, C.M., D.F. Markle, S.B. Reid and M.F. Docker. 2000. Redescription of the presumed extinct Miller Lake Lamprey, Lampetra minima. Copeia 2000:1019-1028.

Malmqvist, B. 1980. The spawning migration of the brook lamprey, Lampetra planeri Block, in a south Swedish stream. Journal of Fish Biology 16:104-114.

Marsden, J. E,*, B. D. Chipman, L. J. Nashett, J. K. Anderson, W. Bouffard, L. Durfey, J. E. Gersmehl, W. F. Schoch, N. R. Staats, and A. Zerrenner. 1999. Sea lamprey control in Lake Champlain. Journal of Great Lakes Research 29(supplement 1):655-676.

McCauley, T. C. 1996. Development of an instream velocity barrier to stop sea lamprey migrations in the Great Lakes. Master’s thesis, University of Manitoba, Winnipeg.

Mesa, M. G., J. M. Bayer, and J. G. Seelye. 2003. Swimming performance and physiological responses to exhaustive exercise in radio-tagged and untagged Pacific lampreys. Transactions of the American Fisheries Society 132:483-492.

Moser, M. L., A. L. Matter, L. C. Stuehrenberg, and T. C. Bjornn, 2002b. Use of an extensive radio reciever network to document Pacific lamprey (Lampetra tridentata) entrance efficiency at fishways in the lower Columbia River, USA. Hydrobiologia, 483:45-53.

Moser, M. L., P. A. Ocker, L. C. Stuehrenberg, and T. C. Bjornn, 2002a. Passage efficiency of adult Pacific lamprey at hydropower dams on the lower Columbia River, USA. Transaction of the American Fisheries Society, 131:956-965.

Moursund RA, DD Dauble, and MD Bleich. 2000. Effects of John Day Dam bypass screens and project operations on the behavior and survival of juvenile Pacific lamprey (Lampetra tridentata). Prepared for the U.S. Army Corps of Engineers, Portland District by Pacific Northwest National Laboratory, Richland, Washington.

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Moursund, R. A, M. D. Bleich, K. D. Ham, and R. P. Mueller. 2003. Evaluation of the effects of extended length submerged bar screens on migrating juvenile Pacific lamprey at John Day Dam in 2002. Final Report of Research, U. S. Army Corps of Engineers, Portland, Oregon.

National Marine Fisheries Service. 1995. Juvenile fish screen criteria. Revised February 16, 1995. Available via the web at: http://www.nwr.noaa.gov/Salmon-Hydropower/FERC/upload/juv-screen-crit.pdf PacifiCorp. 2004. Final Technical Report. Klamath Hydroelectric Project (FERC Project No. 2082). Fish Resources. Portland, Oregon. Version: February 2004

Pletcher, F.T. 1963. The Life History and Distribution of Lampreys in the Salmon and Certain Other Rivers in British Columbia, Canada. Master of Science Thesis. University of British Columbia, Vancouver B.C. 195 p.

Porto, L. M., R. L. McLaughlin, and D. L. G. Noakes. 1999. Low-head barrier dams restrict movements of fishes in two Lake Ontario streams. North American Journal of Fisheries Management 19:1028-1036

Potter, I.C. 1980. Ecology of larval and metamorphosing lampreys. Canadian Journal of Fisheries and Aquatic Science 37:1641-1657.

Schreck CB, MS Fitzpatrick, and DL Lerner. 1999. Determination of passage of juvenile lamprey: development of a tagging protocol. Oregon Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey Biological Resources Division. Oregon State University, Corvallis, Oregon.

Scott, W. B. and E. J. Crossman. 1973. Freshwater fishes of Canada. Fisheries Research Board of Canada Bulletin 184.

Simpson, J. C. and R. L. Wallace. 1978. Fishes of Idaho. University Press of Idaho, Moscow.

Vladykov, V.D. 1973. Lampetra pacifica, a new nonparasitic species of lamprey (Petromyzontidae) from Oregon and California. J. Fish. Res. Board Can. 30: 205-213.

Weeks, H. 1993. Status of Pacific Lamprey. Status Review for Oregon State Sensitive Species Listing. Oregon Department of Fish and Wildlife. Portland, Or.

Wydoski, R. S., and R. R. Whitney. 2003. Inland fishes of Washington. Second edition, revised and expanded. American Fisheries Society, Bethesda, MD, in association with University of Washington Press, Seattle, WA. xiii + 322 pp.

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