San Diego Bay Integrated Natural Resources Management Plan

1.San Diego Bay Integrated Natural Resources Management Plan Public DraftSeptember 1999 September 8, 1999

2. San Diego Bay Integrated Natural Resources Management Plan Public DraftCoastal America Logo Reference: U.S. Department of the Navy, Southwest Division (USDoN, SWDIV). 1999. San Diego Bay IntegratedNatural Resources Management Plan, and San Diego Unified Port District Public Draft. September 1999. San Diego,CA. Prepared by Tierra Data Systems, Escondido, CA.Key words/phrases: Natural Resources Management; NAVORDCENPACDIV; OPNAVINST 5090.1B; NaturalResources Plan; Wildlife Management Plan; Ecosystem Management Plan; Coastal Resources. ii September 8, 1999 3. San Diego Bay Integrated Natural Resources Management Plan Public Draft San Diego Bay Integrated Natural Resources Management Plan This Plan was prepared during 19971999 under the direction and advice of the following:Technical Oversight Committee (TOC) US Navy, Southwest Division Jerry R. Boggs, Ph.D., Chair US Navy, Commander Naval Base Margaret Lenz US Navy, Commander Naval Base Steve Barnhill Port of San Diego Eileen Maher Port of San Diego Melissa Mailander Ogden Environmental, Advisor to Port of San Diego Stacey Baczkowski California Coastal Commission Diana Lilly California Regional Water Quality Control Board Peter Michael California Department of Fish and GameBill Tippets California Department of Fish and GameMarilyn Fluharty Friends of South Bay Wildlife James Peugh National Marine Fisheries Service Robert Hoffman San Diego Association of Governments (SANDAG) Michael McLaughlin The Environmental Trust Don Hunsaker, Ph.D. US Army Corps of EngineersDavid Zoutendyk US Fish and Wildlife Service, Ecological Services Martin Kenney US Fish and Wildlife Service, Refuges Brian Collins Zoological Society of San Diego Jeff Opdycke Science Advisory and Review Team ConsultantElizabeth Copper CSU NorthridgeLarry Allen, Ph.D. Scripps Institution of Oceanography Lisa Levin, Ph.D. Scripps Institution of Oceanography Tom Hayward, Ph.D. Scripps Institution of Oceanography Peter Franks, Ph.D. Naval Installations Oversight Committee (NIOC) US Navy, Southwest Division Jerry R. Boggs, Ph.D., Chair US Navy, Commander Naval Base Margaret Lenz US Navy, Southwest Division Gaston Bordenave US Navy, Southwest Division Kevin McKeagh Naval Air Station North IslandJan Larson Naval Command Center Operations SpecialistDon Lydy Naval Station 32nd Street Mary Ann Flanagan National Park Service, Cabrillo National Monument Carol Knipper US Coast Guard Maritime SafetyLT M.T. Cunninghamiii September 8, 1999 4. San Diego Bay Integrated Natural Resources Management Plan Public Draft This plan was prepared by:Project ManagerPlanner-In-Charge Marine BiologistResearch, GIS, and Layout and DesignWildlife Illustration Tierra Data SystemsSommarstrom and Assoc.Richard Ford, Ph.D. EditingCatherine Lush Peter Else Elizabeth M. Kellogg Sari Sommarstrom, Ph.D. Department of Biology Cynthia Booth208 OKeefe Street 403 South 8th Street 10110 W. Lilac Rd. P.O. Box 719S.D.S.U.Danielle Booth Menlo Park, CA 94025 Laramie, WY 82070 Escondido, CA 92026Etna, CA 960275500 Campanile DriveSherman Jones(650) 327-9201 (307) 755-1837 (760) 749-2247 (530) 467-5783San Diego, CA 92182 James L. Kellogg fax (650) 327-9224 fax (760) 751-9707 Peter McDonaldKeri SalmonScott Snover Cover and Executive Summary photos and illustrations US Navy Southwest Division, Tom Upton and Peter Else. This plan was prepared for the US Department of the Navy, Southwest Division, Naval Facilities Engineering Command, 1220 Pacific Highway, San Diego, CA 92132. Contract No. N68711-95-D-7605/0006. iv September 8, 1999 5. San Diego Bay Integrated Natural Resources Management Plan Public Draft San Diego Bay Integrated Natural Resources Management PlanApproving Officials:Commander, Naval Bases San Diego DateChair, Board of Port Commissioners DateSan Diego Unified Port DistrictField Supervisor DateCarlsbad Field Office U.S. Fish and Wildlife Service Regional Director Date Region V California Department of Fish and Gamev September 8, 1999 6. San Diego Bay Integrated Natural Resources Management Plan Public Draft vi September 8, 1999 7. San Diego Bay Integrated Natural Resources Management Plan Public DraftTable of ContentsExecutive SummaryPart I: Introduction 1.0 Welcome to the Plan1-11.1 The Plan: Why, What, and Where 1-1 1.1.1 The Plans Goal 1-2 1.1.2 Plan Origin 1-2 1.1.3 Purpose 1-5 1.1.4 Planning Zones1-6 1.1.5 Roles of Plan Collaborators 1-6 1.1.6 Missions of US Navy and Port 1-14 1.1.7 Relationship to Other Regional Plans 1-14 1.1.8 Relationship to Local Plans1-151.2 San Diego Bay: An Important and Sensitive Resource1-16 1.2.1 Values 1-16 1.2.2 Key Management Issues1-171.3 Ecosystem Management Framework1-18 1.3.1 Defining Ecosystem Management1-181.4 Strategic Design of Plan1-19 1.4.1 Audience 1-19 1.4.2 Intent of Use1-20 1.4.3 Organization 1-20 1.4.4 Implementation 1-21 1.4.5 Updating 1-22Part II: State of the Bay 2.0 State of the BayEcosystem Resources 2-12.1 Ecoregional Setting2-22.2 Physical Conditions2-2 2.2.1 Climate and Hydrography 2-2 2.2.2 Sediment2-4 2.2.3 Water2-11 2.2.3.1 Turbidity2-11 2.2.3.2 Circulation, Temperature, and Salinity 2-11 2.2.3.3 Residence Time of Water2-12 2.2.3.4 Hydrodynamic Regions of the Bay2-152.3 Water and Sediment Quality2-15 2.3.1 Historical Conditions2-15 2.3.2 Current Conditions 2-18 2.3.2.1 Contaminants 2-18 2.3.2.2 Coliform Contamination 2-21 2.3.2.3 Other Water Quality Conditions 2-21 vii September 8, 1999 8. San Diego Bay Integrated Natural Resources Management Plan Public Draft2.3.3 Regional Comparisons 2-222.3.4 Ecological Effects 2-22 2.4 Bay Habitats2-242.4.1 Deep Subtidal (>20 ft/6 m MLLW)2-282.4.2 Moderately Deep Subtidal (12 to 20 ft (4 to 6 m) MLLW) 2-292.4.3 Shallow Subtidal (2.2 to 12 ft [0.7 to 4 m] MLLW)2-302.4.3.1 Unvegetated Shallow Soft-Bottom2-312.4.3.2 Vegetated Shallow Subtidal 2-332.4.4 Intertidal (+7.8 to 2.2 ft [+2.4 to 0.7 m] MLLW) 2-352.4.4.1 Intertidal Flats 2-362.4.4.2 Salt Marsh 2-392.4.4.3 Artificial Hard Substrate2-462.4.5 Salt Works 2-512.4.6 Upland Transitions 2-522.4.6.1 Beaches and Dunes2-522.4.6.2 Coastal Created Lands and Disturbed Uplands2-552.4.6.3 Freshwater Wetlands and Riparian 2-562.4.6.4 River Mouths 2-57 2.5 Species Assemblages 2-582.5.1 Plankton 2-582.5.1.1 Phytoplankton2-592.5.1.2 Zooplankton2-602.5.1.3 Ichthyoplankton2-612.5.2 Algae2-642.5.2.1 Macroalgae 2-642.5.3 Invertebrates2-662.5.3.1 Invertebrates of Soft Bottom, Unconsolidated Sediment2-672.5.3.2 Invertebrates of Eelgrass Beds 2-712.5.3.3 Invertebrates of Man-made Habitats 2-722.5.3.4 Assessment of Invertebrates as Indicators of Pollution or Habitat Disturbance 2-732.5.4 Fishes 2-752.5.4.1 Description2-752.5.4.2 Species Composition Baywide2-782.5.4.3 Rankings Based on Ecological Index 2-782.5.4.4 Comparison of Total Abundance and Biomass Among Bay Regions and Habitats2-792.5.4.5 Comparisons of Abundance by Region 2-792.5.4.6 Seasonal Changes in Abundance and Biomass2-812.5.4.7 Patterns of Biodiversity and Species Assemblages in Four Regions of the Bay2-822.5.4.8 Functional Groups of Fishes2-832.5.4.9 Species Caught by Commercial or Recreational Fishing 2-922.5.4.10 Warm Water Species in San Diego Bay During El Nio Conditions 2-922.5.4.11 Correlation of Fish Abundance With Environmental Factors2-932.5.4.12 Possible Sensitive Habitats or Nursery Area for Fish in San Diego Bay 2-942.5.5 Birds2-942.5.6 Marine Mammals 2-1092.5.6.1 Mammals of Interest2-1102.5.6.2 Historical Changes in the Bay2-1102.5.6.3 Ecological Roles in the Bay2-1112.5.6.4 Species Accounts 2-1112.5.7 Exotic Marine and Coastal Species2-1132.5.7.1 History and Background 2-1142.5.7.2 Species of Interest2-1152.5.7.3 Sources of Marine and Coastal Exotics2-1192.5.7.4 Ecological and Economic Impacts2-1192.5.7.5 Potential Invasions of Exotics to San Diego Bay2-121 viii September 8, 1999 9. San Diego Bay Integrated Natural Resources Management Plan Public Draft2.6 Sensitive Species 2-122 2.6.1 Federally Listed Species 2-123 2.6.1.1 Green Sea TurtleChelonia mydas2-123 2.6.1.2 California least ternSterna antilarium browni 2-125 2.6.1.3 Light-footed clapper railRallus longirostris levipes2-130 2.6.1.4 California brown pelicanPelecanus occidentalis2-131 2.6.1.5 Western snowy ploverCharadrius alexandrinus nivosus 2-131 2.6.1.6 Sand dune tiger beetleCicindela latesignata latesignata 2-132 2.6.1.7 Salt marsh birds beakCordylanthus maritimus maritimus2-132 2.6.2 State Listed Species and Species of Concern2-1332.7 The Ecosystem as a Functional Whole 2-134 2.7.1 Ecosystem Attributes 2-134 2.7.2 Physical Structure 2-135 2.7.3 Community Organization 2-135 2.7.3.1 Nutrient Cycling 2-137 2.7.3.2 Primary Production 2-137 2.7.3.3 Energy Transfer Through Food Webs2-139 2.7.3.4 Biodiversity 2-141 2.7.4 Disturbance Regimes and Time Scales of Change2-1412.8 State of Ecosystem Health: Information Needs Assessment 2-142 2.8.1 What We Need to Know to Describe Bay Ecosystem Health2-143 2.8.2 What We Currently Understand About Bay Ecosystem Health2-145 3.0 State of the BayHuman Use3-13.1 Ecological History of Human Use 3-3 3.1.1 Summary of Human Use and Change3-33.2 The Bay Regions Human Setting3-7 3.2.1 Area and Population3-7 3.2.2 Land Use and Ownership 3-8 3.2.2.1 Bay Water and Tidelands3-83.3 Current Patterns of Use3-11 3.3.1 Navy Plans and Uses 3-11 3.3.2 Port Plans and Uses 3-17 3.3.3 Local Plans 3-19 3.3.4 Recreation and Tourism Uses 3-19 3.3.5 Navigation3-20 3.3.6 Fisheries 3-203.4 Future Patterns and Plans at the Bay 3-32 3.4.1 Navy3-32 3.4.2 Port3-33 3.4.3 City Plans3-343.5 Economics of Use 3-37 3.5.1 Navy3-37 3.5.2 Port3-38 3.5.3 Fisheries 3-38 3.5.4 Recreation and Tourism3-38 3.5.5 Other Uses3-393.6 Overview of Government Regulation of Bay Activities3-39 3.6.1 Introduction3-39 3.6.2 Federal Agencies and Laws 3-40 3.6.3 State Agencies and Laws 3-43 3.6.4 Local Agencies and Laws 3-47 3.6.5 Project Mitigation Under NEPA and CEQA3-48 ix September 8, 1999 10. San Diego Bay Integrated Natural Resources Management Plan Public Draft Part III: Management Strategies 4.0 Ecosystem Management Strategies4-1 4.1 San Diego Bays Natural Resource Values and Ecosystem Management4-2 4.2 Habitat Protection and Management 4-24.2.1 Strategy by Habitat4-24.2.1.1 Deep Subtidal4-24.2.1.2 Moderately Deep Subtidal 4-64.2.1.3 Unvegetated Shallow Subtidal 4-74.2.1.4 Vegetated Shallow Subtidal4-114.2.1.5 Intertidal Mudflats and Sand Flats4-144.2.1.6 Salt Marsh4-204.2.1.7 Shoreline and Marine Structures 4-254.2.1.8 Salt Works4-314.2.1.9 Upland Transition 4-344.2.1.10 River Mouths and Floodplains 4-364.2.2 Mitigation and Enhancement4-384.2.3 Protected Sites 4-52 4.3 Species Population Protection and Management 4-624.3.1 Exotic Species4-624.3.2 Plankton4-724.3.2.1 Benthic Algae 4-744.3.2.2 Invertebrates 4-754.3.3 Fishes4-774.3.3.1 Harvest Management4-794.3.3.2 Artificial Propagation4-854.3.4 Birds 4-894.3.5 Marine Mammals4-964.3.6 Sensitive Species Special Protections4-1004.3.6.1 Green Sea Turtle 4-1004.3.6.2 California Least Tern4-1054.3.6.3 Light-footed Clapper Rail4-1084.3.6.4 Western Snowy Plover 4-1094.3.6.5 Salt Marsh Birds Beak 4-110 4.4 Ecosystem Approach4-112 5.0 Compatible Use Strategies5-1 5.1 Within Bay Project Strategies 5-25.1.1 Dredge and Fill Projects 5-25.1.2 Ship and Boat Maintenance and Operations5-175.1.3 Shoreline Construction5-265.1.4 Water Surface Use and Shoreline Disturbances5-34 5.2 Watershed Management Strategies5-425.2.1 The Watershed Management Approach 5-425.2.2 Stormwater Management 5-455.2.3 Freshwater Inflow Management5-52 5.3 Cleanup of Bay Use Impacts 5-555.3.1 Remediation of Contaminated Bay Sediments 5-555.3.2 Oil Spill or Hazardous Substance Prevention and CleanUp 5-62 5.4 Cumulative Effects 5-66 5.5 Environmental Education5-69 6.0 Monitoring and Research6-1 6.1 Concepts and Models for Monitoring and Research 6-26.1.1 Tenets for Design of a Monitoring and Research Program 6-26.1.2 Key Management Questions 6-3 6.2 Program Elements6-4 x September 8, 1999 11. San Diego Bay Integrated Natural Resources Management Plan Public Draft6.2.1 Long-term Monitoring for the Bays Ecological Condition and Trend6-56.2.2 Project Monitoring6-166.2.3 Research to Support Management Needs6-196.3 Data Integration, Access, and Reporting 6-23 7.0 Implementation Strategies7-17.1 Achieving Success7-17.2 Components of Implementation 7-37.2.1 Institutional Resources7-37.2.1.1 Existing Organizations 7-37.2.1.2 Potential New Institutions 7-47.2.1.3 Mechanisms 7-47.2.2 Funding Resources7-67.2.2.1 Existing Sources 7-77.2.2.2 Potential New Sources 7-117.2.2.3 Volunteer Contributions 7-117.2.3 Priority Setting7-127.2.3.1 Criteria for Ranking Priority Strategies7-127.2.3.2 Determining Priority Strategies 7-127.2.3.3 Scheduling Priorities 7-127.3 Categories of Implementation7-137.3.1 Strategies by Implementation Category 7-137.4 TOC Priorities for Year One [still in draft]7-14Part IV: References 8.0 Bibliography 8-18.1 Chapter 18-18.2 Chapter 28-28.3 Chapter 3 8-168.4 Chapter 4 8-188.5 Chapter 5 8-268.6 Chapter 6 8-33Part V: Appendixes A. AcronymsA-1 B. GlossaryB-1 C. Oversize Maps C-1 D. Comprehensive Species List of San Diego Bay D-1D.1 ReferencesD-27 E. Species and Their Habitats E-1E.1 ReferencesE-32 F. Narratives on Sensitive Species Not Listed Under Federal or State Endangered Species Acts F-1 G. Ecological History of San Diego Bay G-1xi September 8, 1999 12. San Diego Bay Integrated Natural Resources Management Plan Public Draft H. Draft Policies for Protection of Intertidal Flats and Unvegetated Shallows, Back- ground Paper on Habitat Values of Unvegetated Shallows, and Current Southern Cal- ifornia Eelgrass Mitigation PolicyH-1 H.1 Proposed Policy to Protect Southern California Intertidal Flat Habitat of Bays and Estu-aries (Modeled After Existing Eelgrass Mitigation Policy)H-3 H.2 Proposed Policy to Protect Unvegetated Shallows of Southern California Bays and Estu-aries (Modeled After Existing Southern California Eelgrass Mitigation Policy) H-10 H.3 Background Paper on Soft-Bottom Shallow Subtidal Functions, Values, and Response toDisturbance: A Basis of Policy DevelopmentH-15 H.4 Southern California Eelgrass Mitigation Policy (Adopted July 31, 1991) H-21 H.5 References H-24 xii September 8, 1999 13. September 8, 1999 List of Figures 1-1.Roles of Plan Collaborators.1-13 1-2.Relationship of Planning Terms and Strategy, from Broad to Specific.1-21 2-1.Percent Total Copper Loading to San Diego Bay.2-19 2-2.Percent Total PAH Loading to San Diego Bay. 2-19 2-3.Habitat Definitions Used in this Plan in Relation to Tidal Elevation. 2-27 2-4.Eelgrass Bed. 2-34 2-5.Intertidal Area Exposed Annually in San Diego Bay (1999). 2-36 2-6.Intertidal Flat Community.2-37 2-7.Intertidal Salt MarshSubtidal Interface. 2-40 2-8.Vegetation Patterns in Salt Marsh and Upland Transition Habitats. 2-43 2-9.Artificial Shoreline Environment. 2-46 2-10. Typical Diversity and Abundance of Life in Riprap Compared to a Tide Pool.2-50 2-11. The Beach Environment.2-53 2-12. Abundance of Fishes in San Diego Bay by Station, 19941997.*2-80 2-13. Biomass of Fishes in San Diego Bay by Station, 19941997. 2-80 2-14. Comparison of Fish Density in Vegetated and Nonvegetated Samples. *Statistically significant differences. 2-80 2-15. Fish Density without SS Vegetated vs. Nonvegetated Sites. *Statistically significant differences. 2-80 2-16. Abundance of Fishes in San Diego Bay by Sampling Period.2-81 2-17. Biomass of Fishes in San Diego Bay by Sampling Period.2-81 2-18. Patterns of abundance (left) and biomass (right) of the 10 most common fishes sampled from the northern and southern halves of San Diego Bay (based on Allen 1997). 2-83 2-23. Comparison of Fish Biomass Density in Vegetated and Nonvegetated Samples.* Statistically significant differences.2-89 2-24. Foraging Habitat Partitioning by Birds of San Diego Bay. Dabbling Ducks Forage in Brackish Water, Unrelated to Tidal Elevation.2-97 2-25. First Records of Marine Non-native Species in San Diego Bay. 2-114 2-26. Population Trend in the California Least Tern. 2-129 2-27. Mean Annual Fledging Success for Least Tern Nesting Sites in San Diego Bay and Vicinity.*2-129 2-28. Mean Number of California Least Tern Nests in San Diego Bay and Vicinity, 19941997. 2-129 2-29. Factors Affecting Abundance and Diversity of Birds in San Diego Bay. 2-136 2-30. Simplified San Diego Bay Food Web. 2-138 2-31. This Simplified Food Web Represents Trophic Levels From Producers to a Top Predator, Such as a Harbor Seal. 2-140 3-1.Historic Painting of San Diego Bay by John Stobbart. 3-4 3-2.Regulatory Jurisdictions for In-water Projects in San Diego Bay (For Tidal Definitions, See Figure 2-3).3-41 3-3.Typical Project Processing Flow Chart.3-49 3-4.Comparison of CEQA and NEPA Review Processes (From Bass et al. 1999). 3-51 5-1.Contaminated Sediment Remedial Actions Flowchart (After Barker 1990). 5-59 6-1.Monitoring and Research Program Elements to Support Management Decisions.6-4 6-2.Sample State of San Diego Bay Annual Report.6-25xiii September 8, 1999 14. San Diego Bay Integrated Natural Resources Management Plan Public Draft List of Tables 1-1.Planning Definitions. 1-21 2-1.Estimated trends in total fluvial sediment delivery to San Diego Bay (Smith 1976). 2-4 2-2.Comparison of Known Wastes Discharged into San Diego Bay, 1955 and 1966.2-17 2-3.San Diego Bay: Comparison of Current and Historic Habitat Acreages. 2-24 2-4.Genera and Species of Phytoplankton Reported to Occur in San Diego Bay. 2-59 2-5.Rank Order of Abundance of Zooplankton. 2-62 2-6.South Bay Invertebrate Sampling.2-69 2-7.Ranking of Top Ten Ecological Index Fish Species in San Diego Bay 2-78 2-8.Total Number of Individuals and Biomass (g) of Fish Species Captured in the North Bay (Station 1), July 1994April 1997. 2-84 2-9.Total Number of Individuals and Biomass (g) of Fish Species Taken at the North-Central Bay (Station 2), July 1994April 1997. 2-85 2-10. Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay (Station 3), July 1994April 1997. 2-86 2-11. Total Number of Individuals and Biomass (g) of fish Species Taken at the South Bay (Station 4), July 1994April 1997. 2-87 2-12. Species Closely Associated with Eelgrass Beds.2-87 2-13. San Diego Bay Fish Taken in Subtidal Eelgrass Bed Habitat.2-88 2-14. San Diego Bay Fish Species Taken in Subtidal Unvegetated, Unconsolidated Sediment Habitat.2-88 2-15. San Diego Bay Fish Species Taken in Deep Subtidal Habitats. 2-90 2-16. Fish Species Associated with Artificial Habitats in San Diego Bay.2-91 2-17. Indigenous Bay-estuarine Species. 2-91 2-18. Fish Species of San Diego Bay Taken by Recreational and Commercial Fishermen. 2-93 2-19. Historic Changes in Bay Bird Populations. 2-96 2-20. Comparison of Three Concurrent Surveys of Bay Avifauna Conducted in 1993, and One 1994 Survey of Central Bay. 2-98 2-21. Cumulative Observations of the Most Abundant Waterfowl., 2-103 2-22. Cumulative Observations of the Most Abundant Shorebirds. 2-105 2-23. Cumulative Observations of the Most Abundant Sea Birds.2-106 2-24. Cumulative Observations of Herons and Egrets.2-107 2-25. Nesting/Breeding Areas of Bay Bird Species (and Number of Nests or Pairs Where Reported).2-109 2-26. List of Exotic Marine Animals Found in San Diego Bay, Their Probable Source, Problems, or Effects Caused, and Other Comments. 2-115 2-27. Exotic Coastal Plants at San Diego Bay.2-118 2-28. Sensitive Species, Their Habitats and Risk Factors in San Diego Bay. 2-122 2-29. Colony Sizes, Reproduction, and Fledging Success at Least Tern Nesting Sites in San Diego Bay, Mission Bay, and Tijuana Slough. 2-130 2-30. Information Needs for Ecosystem Management of San Diego Bay. 2-144 3-1.San Diego Bay Tidelands by Ownership (uncorrected for approximately 1490 acres of land and water transferred from private and state holdings to USFWS, 1999). 3-8 3-2.Natural Resource Management Plans and Approval Dates for the San Diego Bay Area.3-12 3-3.US Navy, US Coast Guard, and US Marine Corps Uses of San Diego Bay by Organization. 3-15 3-4.San Diego Bay Port Master Plan Water Use Mapping Definitions, as Seen in Map 3-4. 3-18 3-5.Boat Traffic Patterns.3-29xiv September 8, 1999 15. San Diego Bay Integrated Natural Resources Management Plan Public Draft 3-6.Boat Traffic Patterns. 3-30 3-7.Future Navy Plans for In-water Projects. 3-33 3-8.Proposed Capital Improvement Program Projects for Ports Tidelands, 19992008, Pertinent to this INRMP. 3-37 3-9.Uniform Tourist Tax Collections, FYs 19881996, for Cities in San Diego Bay Region.3-39 3-10. Federal Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-42 3-11. State Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-44 3-12. Local Agencies with Responsibilities for Natural Resources in San Diego Bay. 3-47 3-13. Examples of Marine Impact Mitigations Described for Recent Bay Projects (Based on EIRs, EISs, and EAs).3-53 4-1.Salt Marsh Mitigation Standards. 4-22 4-2.Attributes That Should be Researched to Determine Their Level of Importance, Practicality, and Cost-effectiveness for Use as a Performance Measure. 4-47 4-3.Possible Enhancement Opportunity Areas.4-49 4-4.In-water Project Preplanning Checklist 4-51 4-5.Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection from Development [table to be completed to include changes]. 4-53 4-6.State Marine Protection Area (MPA) Options: Intent, Methods, Examples. 4-60 4-7.Sport Fishing Limits on Fish and Invertebrate Species of San Diego Bay (CDFG 1997).4-81 4-8.Recreational Angler Catch Sampling List of Major Species for Inland Marine San Diego County, 19931998.4-82 4-9.Historic and Current Habitat Acreages in Four Bay Regions.4-115 5-1.Summary of Existing and Potential Dredging Projects and Disposal Methods since 1988.5-4 5-2.Provisions of the CCA Relevant to Dredge Disposal.5-7 5-3.Biological Effects of Various Dredging Methods Available in San Diego Bay. 5-12 5-4.Bay Surface Area Occupied by Fixed Structures (Docks, Piers, Wharves) and by Ships and Boats Using these Sites. 5-28 5-5.Quantity and Type of Bay Habitat Surface Covered by Docks, Piers, Wharves, and Docked Ships and Boats at Maximum Use.5-28 5-6.Projected Net Gain or Loss in Bay Coverage from Navy Wharves, Piers, and Floating Docks. 5-29 5-7.Totals and Averages for Specific Disturbance Types for the Entire South Bay Study Area.5-40 5-8.Percentage of Birds Sampled Avoiding Survey Boat by Distance Category in Central San Diego Bay.5-40 5-9.Federal and State Statutes Affecting Management of Contaminated Sediment.5-57 6-1.Priority Monitoring Parameters Agreed Upon by the San Diego Bay Interagency Water Quality Panel.6-7 6-2.Examples of the Proposed Use of Ecological Indicators to Learn about San Diego Bays Condition and Trend 6-9 6-3.Priority Long-term Monitoring Parameters.6-12 6-4.List of Candidate Target Species for Supporting Long-term Monitoring (and for Project Planning). 6-14 6-5.Research (or Pre-research) Interests Identified by TOC (April 21, 1999). 6-20 7-1.Existing Institutions to Implement the Plan (TOC Members Noted with *). 7-3 7-2.New Organization Options for Plan Implementation. 7-5 7-3.Examples of Formal and Informal Institutional Mechanisms for Implementation.7-6 7-4.Available Primary Funding Sources for Plan Implementation.7-7 7-5.Ideas for New Funding Sources for Bay Ecosystem Management.7-11 7-6.General Strategies by Implementation Category [to be completed]. 7-13 E-1.Plant Species and Their Habitats. E-3 E-2.San Diego Invertebrate Habitats.E-9 E-3.San Diego Bay Fishes: Their Habitat and Feeding Strategies.E-21 E-4.San Diego Bay Birds: Their Diet, Status, and Habitat.E-26 G-1.Ecological History of San Diego Bay. G-3xv September 8, 1999 16. San Diego Bay Integrated Natural Resources Management Plan Public Draft List of Maps 1-1.San Diego Bay, the Conceptual Watershed Influence Zone, in the Southern California Bight. 1-7 1-2.San Diego Bay INRMP Footprint and Functional Planning Zone. 1-9 1-3.San Diego Bay INRMP Functional Planning Footprint and Conceptual Watershed Influence Zone. 1-11 2-1.Recent Topography of San Diego Bay Floor. 2-5 2-2.Cumulative History of Dredge and Fill Activity in San Diego Bay.2-7 2-3.Percent Fine Sediments (Silt and Clay) on the Bay Floor.2-9 2-4.Half-life of Water Residing in the Bay with Different Tidal Amplitudes.2-13 2-5.San Diego Bay Benthic Community Quality Analysis.2-25 2-6.Salt Marsh and Upland Transition Adjacent to San Diego Bay.2-41 2-7.Shoreline Structures of San Diego Bay. 2-47 2-8.Relative Abundance of Birds Based on Three Surveys Conducted in 19931994. 2-99 2-9.Biodiversity of Birds Based on Three Surveys Conducted in 19931994.2-101 2-10. Least Tern Foraging and Nesting Areas in San Diego Bay. 2-127 3-1.San Diego Bay Historic Habitat Footprint (1859), with Current Shoreline Overlay.3-5 3-2.San Diego Bay Regional Land Use.3-9 3-3.Local Planning Jurisdictions of San Diego Bay Environs.3-13 3-4.San Diego Bay Port Jurisdiction Master Plan Water Use Designations.3-21 3-5.San Diego Bay Marinas, Docks, and Public Recreational Areas. 3-23 3-6.San Diego Bay Water Navigation Systems and Restricted Areas. 3-25 3-7.Boat Traffic Patterns on San Diego Bay (Refer to Table 3-6 for Detailed Explanations of this Map). 3-27 3-8.San Diego Bay US Naval Facilities and Planned Capital Improvements Summary (19972002).3-35 4-1.Past Mitigation Projects in San Diego Bay. 4-45 4-2.Protected Marine and Coastal Habitat in San Diego Bay1998.4-57 5-1.San Diego Bay Oil Spills Reported to US Coast Guard (19931996). 5-63 C-1.Habitats of San Diego Bay.C-3 C-2.Mean Numerical Density of All Fish Species January Samples, 19941997.C-5 C-3.Mean Numerical Density of All Fish Species July Samples, 19941997. C-7 C-4.Mean Biomass Density of All Fish Species January Samples, 19941997.C-9 C-5.Mean Biomass Density of All Fish Species July Samples, 19941997.C-11 C-6.Potential Restoration and Enhancement Projects in San Diego Bay. C-13 xvi September 8, 1999 17. San Diego Bay Integrated Natural Resources Management Plan Public Draft List of Photos 1-1.Aerial Photo of San Diego Bay Region.1-3 1-2.San Diego Bay.1-18 2-1.South Bay Mudflat Adjoining Northernmost Levee of Salt Works.2-1 2-2.Sea Lions Napping on Buoy.2-28 2-3.Birds Rafting.2-30 2-4.Ray.2-31 2-5.Eelgrass bed. 2-34 2-6.Small Mudflat Adjacent to Delta Beach, Showing Sediment Churned Up At High Tide (1998). 2-38 2-7.Mudflat of South Bay. 2-39 2-8.Invertebrate in Riprap. 2-49 2-9.Salt Works. 2-51 2-10. Sand Hummocks with Ambrosia Chamissonis.2-54 2-11. Dune Vegetation in Flower.2-55 2-12. Sweetwater Channel. 2-57 2-13. Wandering Sponge (Tetilla mutabilis) with the Ectoprot Zoobotryon verticillatum and Algae, Including Gracilaria. 2-71 2-14. Anemones and Tube-forming Polychaete Worms Living on Man-made Surface (Sunken Boat).2-73 2-15. Killifish.2-75 2-16. Beldings Savannah Sparrow on Pickleweed.2-134 3-1.San Diego Bay Pier.3-1 3-2.Aerial Photos of San Diego Bay 1928. 3-2 3-3.North Island 1936. 3-4 3-4.US Navy Cruiser and Destroyer.3-12 3-5.San Diego Bay.3-17 3-6.Bait for Fishing Available in the Bay.3-31 3-7.City of San Diego.3-33 4-1.Egret at Low Tide. 4-1 4-2.Bay Traffic. 4-3 4-3.Crater Produced by a Tube Worm or Bivalve Mollusk. 4-8 4-4.Eelgrass Bed. 4-12 4-5.Mudflat.4-15 4-6.San Diego Bay Salt Marsh. 4-21 4-7.Black skimmers on Salt Works Levee. 4-31 4-8.Planting Eelgrass.4-38 4-9.Black-necked Stilt. 4-42 4-10. Heron Park Sign at NASNI. 4-52 4-11. Heron.4-89 4-12. Green Sea Turtle.4-100 4-13. California Least Tern. 4-105 5-1.Coronado Bridge Over San Diego Bay.5-1 5-2.Dredging in San Diego Bay. 5-3 5-3.Sailing on San Diego Bay. 5-26xvii September 8, 1999 18. San Diego Bay Integrated Natural Resources Management Plan Public Draft 5-4.Boat Ramp with Riprap. 5-28 5-5.Waterbirds of the Bay. 5-34 5-6.Jet Skier with Navy Carrier. 5-35 5-7.Waterbirds and Boats on San Diego Bay. 5-37 5-8.Riprap Armoring near Coronado Cays.5-67 6-1.Arctic Tern.6-1 7-1.Shells of San Diego Bay.7-1 xviii September 8, 1999 19. San Diego Bay Integrated Natural Resources Management Plan September 2000 September 2000 20. San Diego Bay Integrated Natural Resources Management PlanReference: U.S. Department of the Navy, Southwest Division (USDoN, SWDIV) and San Diego Unified Port District(SDUPD). San Diego Bay Integrated Natural Resources Management Plan, September 2000. San Diego, CA.Prepared by Tierra Data Systems, Escondido, CA.Key words/phrases: Natural Resources Management; NAVORDCENPACDIV; OPNAVINST 5090.1B; NaturalResources Plan; Wildlife Management Plan; Ecosystem Management Plan; Coastal Resources.No part of this book may be reproduced in any form or by any electronic or mechanical means without permissionof the U.S. Department of the Navy, Southwest Division and San Diego Unified Port Districtii September 2000 21. San Diego Bay Integrated Natural Resources Management Plan San Diego Bay Integrated Natural Resources Management Plan This Plan was prepared during 19972000 under the direction and advice of the following:Technical Oversight Committee US Navy, Southwest DivisionJerry R. Boggs, Ph.D., Chair US Navy, Commander Naval Region SouthwestMargaret Lenz, Tamara Conkle Port of San DiegoEileen Maher Port of San DiegoMelissa Mailander Ogden Environmental, Advisor to Port of San DiegoStacey Baczkowski California Coastal CommissionDiana Lilly California Regional Water Quality Control BoardPeter Michael California Department of Fish and Game Bill Tippets California Department of Fish and Game Marilyn Fluharty Friends of South Bay WildlifeJames Peugh National Marine Fisheries ServiceRobert Hoffman San Diego Association of Governments Michael McLaughlin The Environmental TrustDon Hunsaker, Ph.D. US Army Corps of Engineers David Zoutendyk US Fish and Wildlife Service, Ecological ServicesMartin Kenney US Fish and Wildlife Service, RefugesBrian Collins Zoological Society of San DiegoJeff Opdycke Science Advisory and Review Team Consultant Elizabeth Copper CSU Northridge Larry Allen, Ph.D. Scripps Institution of OceanographyLisa Levin, Ph.D. Scripps Institution of OceanographyTom Hayward, Ph.D. Scripps Institution of OceanographyPeter Franks, Ph.D. Naval Installations Oversight Committee US Navy, Southwest DivisionJerry R. Boggs, Ph.D., Chair US Navy, Commander Naval Region SouthwestMargaret Lenz US Navy, Southwest DivisionGaston Bordenave US Navy, Southwest DivisionKevin McKeag Naval Air Station North Island Jan Larson Naval Command Center Operations Specialist Don Lydy Naval Station 32nd StreetMary Ann Flanagan National Park Service, Cabrillo National MonumentCarol Knipper US Coast Guard Maritime Safety Lt. M.T. Cunninghamiii September 2000 22. San Diego Bay Integrated Natural Resources Management Plan This plan was prepared by:Project ManagerPlanner-In-Charge Marine BiologistResearch, GIS, andLayout and DesignWildlife Illustration Tierra Data SystemsSommarstrom and Assoc.Richard Ford, Ph.D. Editing Catherine Lush Peter Else Elizabeth M. Kellogg Sari Sommarstrom, Ph.D. Department of Biology Cynthia Booth 208 OKeefe Street 403 South 8th Street 10110 W. Lilac Rd. P.O. Box 719S.D.S.U.Danielle BoothMenlo Park, CA 94025 Laramie, WY 82070 Escondido, CA 92026Etna, CA 960275500 Campanile DriveSherman Jones (650) 327-9201 (307) 755-1837 (760) 749-2247 (530) 467-5783San Diego, CA 92182 James L. Kelloggfax (650) 327-9224 fax (760) 751-9707 Nancy McDonaldPeter McDonaldKeri SalmonScott Snover Cover and Executive Summary photos and illustrations US Navy Southwest Division, Tom Upton or Peter Else. This plan was prepared for the US Department of the Navy, Southwest Division, Naval Facilities Engineering Command, 1220 Pacific Highway, San Diego, CA 92132. Contract No. N68711-95-D-7605/0006. iv September 2000 23. San Diego Bay Integrated Natural Resources Management Plan San Diego Bay Integrated Natural Resources Management PlanApproving Officials:Commander, Naval Bases San Diego DateChair, Board of Port Commissioners DateSan Diego Unified Port DistrictField Supervisor Date Carlsbad Field Office U.S. Fish and Wildlife ServiceRegional DirectorDateRegion VCalifornia Department of Fish and GameRegional Administrator Date National Marine Fisheries Servicev September 2000 24. San Diego Bay Integrated Natural Resources Management Plan vi September 2000 25. San Diego Bay Integrated Natural Resources Management Plan Table of Contents Executive SummaryPart I: IntroductionChapter 1.0 Welcome to the Plan1-1 1.1 The Plan: Why, What, and Where 1-11.1.1 The Plans Goal 1-21.1.2 Plan Origin 1-21.1.3 Purpose 1-41.1.4 Planning Zones1-51.1.5 Roles of Plan Collaborators 1-51.1.6 Missions of US Navy and Port 1-101.1.7 Relationship to Other Regional Plans 1-101.1.8 Relationship to Local Plans1-11 1.2 San Diego Bay: An Important and Sensitive Resource1-121.2.1 Values 1-121.2.2 Key Management Issues1-13 1.3 Ecosystem Management Framework1-141.3.1 Defining Ecosystem Management1-14 1.4 Strategic Design of Plan1-151.4.1 Audience 1-151.4.2 Intent of Use1-161.4.3 Organization 1-161.4.4 Implementation 1-171.4.5 Updating 1-18Part II: State of the BayChapter 2.0 State of the BayEcosystem Resources 2-1 2.1 Ecoregional Setting2-2 2.2 Physical Conditions2-2 2.2.1 Climate and Hydrography2-2 2.2.2 Sediment 2-4 2.2.3 Water2-82.2.3.1 Turbidity 2-82.2.3.2 Circulation, Temperature, and Salinity2-82.2.3.3 Residence Time of Water 2-92.2.3.4 Hydrodynamic Regions of the Bay2-10 2.3 Water and Sediment Quality2-10 2.3.1 Historical Conditions 2-10 2.3.2 Current Conditions2-142.3.2.1 Contaminants 2-142.3.2.2 Coliform Contamination 2-172.3.2.3 Other Water Quality Conditions 2-17vii September 2000 26. San Diego Bay Integrated Natural Resources Management Plan 2.3.3 Regional Comparisons 2-18 2.3.4 Ecological Effects 2-182.4 Bay Habitats2-20 2.4.1 Deep Subtidal2-20 2.4.2 Moderately Deep Subtidal 2-25 2.4.3 Shallow Subtidal 2-26 2.4.3.1 Unvegetated Shallow Soft Bottom2-26 2.4.3.2 Vegetated Shallow Subtidal 2-29 2.4.4 Intertidal 2-31 2.4.4.1 Intertidal Flats 2-32 2.4.4.2 Salt Marsh 2-35 2.4.4.3 Artificial Hard Substrate2-41 2.4.5 Salt Works 2-44 2.4.6 Upland Transitions 2-46 2.4.6.1 Beaches and Dunes2-47 2.4.6.2 Coastal Created Lands and Disturbed Uplands2-49 2.4.6.3 Freshwater Wetlands and Riparian 2-50 2.4.6.4 River Mouths 2-512.5 Species Assemblages 2-52 2.5.1 Plankton 2-52 2.5.1.1 Phytoplankton2-53 2.5.1.2 Zooplankton2-55 2.5.1.3 Ichthyoplankton2-55 2.5.2 Algae2-58 2.5.2.1 Macroalgae 2-58 2.5.3 Invertebrates2-60 2.5.3.1 Invertebrates of Soft Bottom, Unconsolidated Sediment2-61 2.5.3.2 Invertebrates of Eelgrass Beds 2-65 2.5.3.3 Invertebrates of Man-made Habitats 2-66 2.5.3.4 Assessment of Invertebrates as Indicators of Pollution or HabitatDisturbance 2-67 2.5.4 Fishes 2-69 2.5.4.1 Description2-69 2.5.4.2 Species Composition Baywide2-72 2.5.4.3 Rankings Based on Ecological Index 2-72 2.5.4.4 Comparison of Total Abundance and Biomass Among Bay Regions2-73 2.5.4.5 Comparisons of Species Abundance and Biomass by Region 2-73 2.5.4.6 Seasonal Changes in Abundance and Biomass2-78 2.5.4.7 Patterns of Biodiversity and Species Assemblages in Four Regionsof the Bay2-79 2.5.4.8 Functional Groups of Fishes2-83 2.5.4.9 Species Caught by Commercial or Recreational Fishing 2-87 2.5.4.10 Warm Water Fishes in San Diego Bay During El Nio 2-89 2.5.4.11 Correlation of Fish Abundance With Environmental Factors2-89 2.5.4.12 Possible Sensitive Habitats or Nursery Area for Fishesin San Diego Bay2-90 2.5.5 Birds2-90 2.5.6 Marine Mammals2-104 2.5.6.1 Mammals of Interest 2-104 2.5.6.2 Historical Changes in the Bay 2-105 2.5.6.3 Ecological Roles in the Bay 2-105 2.5.6.4 Species Accounts2-106 2.5.7 Exotic Marine and Coastal Species 2-108 2.5.7.1 History and Background2-109 2.5.7.2 Species of Interest 2-110 2.5.7.3 Sources of Marine and Coastal Exotics 2-110 2.5.7.4 Ecological and Economic Impacts 2-114 2.5.7.5 Potential Invasions of Exotics to San Diego Bay 2-115 viii September 2000 27. San Diego Bay Integrated Natural Resources Management Plan 2.6 Sensitive Species2-1172.6.1 Federally Listed Species2-1182.6.1.1 Green Sea Turtle2-1182.6.1.2 California least tern 2-1212.6.1.3 Light footed clapper rail 2-1242.6.1.4 California brown pelican2-1252.6.1.5 Western snowy plover2-1262.6.1.6 Sand dune tiger beetle2-1272.6.1.7 Salt marsh birds beak2-1272.6.2 State Listed Species and Species of Concern 2-128 2.7 The Ecosystem as a Functional Whole2-1292.7.1 Ecosystem Attributes2-1292.7.2 Physical Structure2-1312.7.3 Community Organization2-1312.7.3.1 Nutrient Cycling2-1332.7.3.2 Primary Production2-1332.7.3.3 Energy Transfer Through Food Webs 2-1342.7.3.4 Biodiversity2-1362.7.4 Disturbance Regimes and Time Scales of Change 2-136 2.8 State of Ecosystem Health: Information Needs Assessment2-1372.8.1 What We Need to Know to Describe the State of the Bay Ecosystem 2-1382.8.2 What We Currently Understand About Bay Ecosystem Health 2-139Chapter 3.0 State of the BayHuman Use 3-1 3.1 Ecological History of Human Use3-33.1.1 Summary of Human Use and Change 3-3 3.2 The Bay Regions Human Setting 3-63.2.1 Area and Population 3-63.2.2 Land Use and Ownership3-73.2.2.1 Bay Water and Tidelands 3-7 3.3 Current Patterns of Use3-93.3.1 Navy Plans and Uses 3-93.3.2 Port Plans and Uses3-143.3.3 Local Plans3-173.3.4 Recreation and Tourism Uses3-173.3.5 Navigation 3-213.3.6 Fisheries3-21 3.4 Future Patterns and Plans at the Bay3-243.4.1 Navy 3-243.4.2 Port 3-263.4.3 City Plans 3-28 3.5 Economics of Use3-283.5.1 Navy 3-283.5.2 Port 3-283.5.3 Fisheries3-293.5.4 Recreation and Tourism 3-293.5.5 Other Uses 3-30 3.6 Overview of Government Regulation of Bay Activities 3-303.6.1 Introduction 3-303.6.2 Federal Agencies and Laws3-323.6.3 State Agencies and Laws3-343.6.4 Local Agencies and Laws3-383.6.5 Project Mitigation Under NEPA and CEQA 3-39 ix September 2000 28. San Diego Bay Integrated Natural Resources Management Plan Part III: Management StrategiesChapter 4.0 Ecosystem Management Strategies 4-14.1 San Diego Bays Natural Resource Values and Ecosystem Management4-24.2 Habitat Protection and Management 4-2 4.2.1 Strategy by Habitat4-2 4.2.1.1 Deep Subtidal4-2 4.2.1.2 Moderately Deep Subtidal 4-6 4.2.1.3 Unvegetated Shallow Subtidal 4-7 4.2.1.4 Vegetated Shallow Subtidal4-11 4.2.1.5 Intertidal Flats4-14 4.2.1.6 Salt Marsh4-19 4.2.1.7 Artificial Hard Substrate 4-24 4.2.1.8 Salt Works4-30 4.2.1.9 Upland Transitions4-33 4.2.1.10 River Mouths and Floodplains 4-36 4.2.2 Mitigation and Enhancement4-37 4.2.3 Protected Sites 4-504.3 Species Population Protection and Management 4-61 4.3.1 Exotic Species4-61 4.3.2 Plankton4-72 4.3.2.1 Benthic Algae 4-73 4.3.2.2 Invertebrates 4-74 4.3.3 Fishes4-76 4.3.3.1 Harvest Management4-78 4.3.3.2 Artificial Propagation4-84 4.3.4 Birds 4-88 4.3.5 Marine Mammals4-95 4.3.6 Sensitive Species Special Protections 4-99 4.3.6.1 Green Sea Turtle4-99 4.3.6.2 California Least Tern4-104 4.3.6.3 Light-footed Clapper Rail4-107 4.3.6.4 Western Snowy Plover 4-108 4.3.6.5 Salt Marsh Birds Beak 4-1094.4 Ecosystem Approach4-111Chapter 5.0 Compatible Use Strategies 5-15.1 Within-Bay Project Strategies 5-25.1.1 Dredge and Fill Projects5-25.1.2 Ship and Boat Maintenance and Operations 5-175.1.3 Shoreline Construction 5-265.1.4 Water Surface Use and Shoreline Disturbances 5-355.2 Watershed Management Strategies5-435.2.1 The Watershed Management Approach5-435.2.2 Storm water Management 5-465.2.3 Freshwater Inflow Management 5-555.3 Cleanup of Bay Use Impacts 5-585.3.1 Remediation of Contaminated Sediments5-585.3.2 Oil Spill or Hazardous Substance Prevention and CleanUp5-665.4 Cumulative Effects 5-695.5 Environmental Education5-72Chapter 6.0 Monitoring and Research 6-16.1 Concepts and Models for Monitoring and Research 6-26.1.1 Tenets for Design of a Monitoring and Research Program6-26.1.2 Key Management Questions6-36.2 Program Elements6-4 x September 2000 29. San Diego Bay Integrated Natural Resources Management Plan 6.2.1 Long-term Monitoring for the Bays Ecological Condition and Trend6-5 6.2.2 Project Monitoring6-17 6.2.3 Research to Support Management Needs6-19 6.3 Data Integration, Access, and Reporting 6-24Chapter 7.0 Implementation Strategies7-1 7.1 Achieving Success7-2 7.2 Components of Implementation 7-3 7.2.1 Institutional Resources7-37.2.1.1 Existing Organizations7-37.2.1.2 Potential New Institutions and Mechanisms 7-4 7.2.2 Funding Resources7-67.2.2.1 Existing Sources7-77.2.2.2 Potential New Sources7-117.2.2.3 Volunteer Contributions7-12 7.3 Proposed Organizational Structure 7-12 7.4 Priority Setting7-15 7.4.1 Criteria for Ranking Priority Strategies and Projects 7-15 7.4.2 Scheduling Priorities 7-16 Part IV: ReferencesChapter 8.0 Bibliography 8-1 8.1 Chapter 18-1 8.2 Chapter 28-2 8.3 Chapter 3 8-16 8.4 Chapter 4 8-18 8.5 Chapter 5 8-26 8.6 Chapter 6 8-33 Part V: AppendicesA. AcronymsA-1B. GlossaryB-1C. Oversize Maps C-1D. Comprehensive Species List of San Diego Bay D-1 D.1 ReferencesD-27E. Species and Their HabitatsE-1 E.1 ReferencesE-29F. Narratives on SensitiveSpecies Not Listed Under Federal or State Endangered Species Acts F-1 F.1 ReferencesF-10 G. Ecological History of San Diego BayG-1 G.1 References G-8H. Habitat Protection Policies: Preliminary Concepts H-1 H.1 Draft Policy for Protection of Intertidal FlatsH-3xi September 2000 30. San Diego Bay Integrated Natural Resources Management Plan H.2 Draft Policy for Protection of Unvegetated ShallowsH-10 H.3 Background Paper on Habitat Values of Unvegetated Shallows H-14 H.4 Current Southern California Eelgrass Mitigation Policy H-20 H.5 References H-23I. Public Comments and ResponsesI-1 xii September 2000 31. San Diego Bay Integrated Natural Resources Management Plan List of Figures 1-1. Roles of Plan Collaborators. 1-9 1-2. Relationship of Planning Terms and Strategy, from Broad to Specific.1-17 2-1. Percent Total Copper Loading to San Diego Bay.2-15 2-2. Percent Total PAH Loading to San Diego Bay. 2-16 2-3. Habitat Definitions Used in this Plan in Relation to Tidal Elevation. 2-22 2-4. Eelgrass Bed. 2-30 2-5. Intertidal Area Exposed Annually in San Diego Bay (1999). 2-32 2-6. Intertidal Flat Community.2-33 2-7. Intertidal Salt MarshSubtidal Interface. 2-36 2-8. Vegetation Patterns in Salt Marsh Habitats. 2-38 2-9. Artificial Shoreline Environment. 2-41 2-10.Typical Diversity and Abundance of Life in a Tide Pool (top) Compared to That of Life in Riprap (bottom). 2-45 2-11.The Beach Environment.2-47 2-12.Abundance of Fishes in San Diego Bay by Station, 19941999. 2-74 2-13.Biomass of Fishes in San Diego Bay by Station, 19941999. 2-74 2-14.Abundance of Fishes in San Diego Bay by Sampling Period.2-79 2-15.Biomass of Fishes in San Diego Bay by Sampling Period.2-79 2-16.Abundant Fish Species of North Bay. 2-80 2-17.Fishes Distinctive of North Bay, and Not Typically Found in South Bay.2-80 2-18.Abundant Fish Species of South Bay. 2-81 2-19.Fishes Distinctive of South Bay, and Not Typically Found in North Bay.2-81 2-20.Patterns of Abundance (left) and Biomass (right) of the Ten Most Common Fishes sampled from theNorthern and Southern Halves of San Diego Bay (based on Allen 1999).2-82 2-21.Comparison of Fish Numerical Density in Vegetated and Unvegetated Samples.2-85 2-22.Comparison of Fish Biomass Density in Vegetated and Unvegetated Sites.2-85 2-23.Foraging Habitat Partitioning by Birds of San Diego Bay. Dabbling Ducks Forage in Brackish Water,Unrelated to Tidal Elevation. 2-93 2-24.First Records of Marine Non-native Species in San Diego Bay. 2-109 2-25.Population Trend in the California Least Tern. 2-123 2-26.Mean Annual Fledging Success for Least Tern Nesting Sites in San Diego Bay and Vicinity. 2-123 2-27.Mean Number of California Least Tern Nests in San Diego Bay and Vicinity, 19941997. 2-124 2-28.Factors Affecting Abundance and Diversity of Birds in San Diego Bay. 2-130 2-29.Simplified San Diego Bay Food Web. 2-132 2-30. Simplified Food Web Represents Trophic Levels From Producers to Top Predator, Such as a Harbor Seal.2-135 3-1. Historic Painting of San Diego Bay by John Stobbart. 3-5 3-2. Regulatory Jurisdictions for In-water Projects in San Diego Bay (For Tidal Definitions, See Figure 2-3).3-31 3-3. Typical Project Processing Flow Chart.3-40 3-4. Comparison of CEQA and NEPA Review Processes (From Bass et al. 1999). 3-41 5-1. Contaminated Sediment Remedial Actions Flowchart (After Barker 1990). 5-62 6-1. Monitoring and Research Program Elements to Support Management Decisions.6-4 6-2. Sample State of San Diego Bay Annual Report.6-27 7-1. Proposed Stakeholders Committee - Subcommittee Organizational Structure. 7-13xiii September 2000 32. San Diego Bay Integrated Natural Resources Management Plan xiv September 2000 33. San Diego Bay Integrated Natural Resources Management Plan List of Tables 1-1. Planning Definitions.1-17 2-1. Estimated trends in total fluvial sediment delivery to San Diego Bay (Smith 1976).2-4 2-2. Comparison of Known Wastes Discharged into San Diego Bay, 1955 and 1966. 2-13 2-3. San Diego Bay: Comparison of Current and Historic Habitat Acreages 2-23 2-4. Genera and Species of Phytoplankton Reported in San Diego Bay.,2-54 2-5. Rank Order of Abundance of Zooplankton., 2-56 2-6. South Bay Invertebrate Sampling 1976-1989. 2-63 2-7. Ranking of Top Ten Ecological Index Fish Species in San Diego Bay. 2-73 2-8. Total Number of Individuals and Biomass (g) of Fish Species Captured in the North Bay (Station 1),July 1994April 1999.2-75 2-9. Total Number of Individuals and Biomass (g) of Fish Species Taken in the North-Central Bay (Station 2),July 1994April 1999.2-76 2-10.Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay (Station 3),July 1994April 1999.2-77 2-11.Total Number of Individuals and Biomass (g) of Fish Species Taken in the South Bay (Station 4),July 1994April 1999.2-78 2-12. San Diego Bay Fish Species Closely Associated with Subtidal Eelgrass Habitat. 2-83 2-13.San Diego Bay Fish Species Taken in Subtidal Eelgrass Bed Habitat. 2-84 2-14.San Diego Bay Fish Species Taken in Subtidal Unvegetated, Unconsolidated Sediment Habitat. 2-84 2-15.San Diego Bay Fish Species Taken in Deep Subtidal Habitats.2-86 2-16.San Diego Bay Fish Species Associated with Artificial, Man-made Habitats.2-86 2-17.Indigenous Bay-estuarine Species.2-87 2-18.Fish Species of San Diego Bay Taken by Recreational and Commercial Fishermen.2-88 2-19.Historic Changes in Bay Bird Populations.2-91 2-20.Comparison of Three Concurrent Surveys of Bay Avifauna Conducted in 1993, and One 1994 Survey ofCentral Bay. 2-93 2-21.Cumulative Observations of the Most Abundant Waterfowl.2-97 2-22.Cumulative Observations of the Most Abundant Shorebirds. 2-99 2-23.Cumulative Observations of the Most Abundant Sea Birds. 2-100 2-24.Cumulative Observations of Herons and Egrets. 2-101 2-25.Nesting/Breeding Areas of Bay Birds (and Number of Nests or Pairs Where Reported).2-103 2-26.Exotic Marine Algae and Coastal Plants at San Diego Bay.2-111 2-27.List of Exotic Marine Animals Found in San Diego Bay, Their Probable Source, Problems, or EffectsCaused, and Other Comments. 2-112 2-28.Sensitive Species, Their Habitats and Risk Factors in San Diego Bay.2-117 2-29.Colony Sizes, Reproduction, and Fledging Success at Least Tern Nesting Sites in San Diego Bay, MissionBay, and Tijuana Slough.2-124 2-30.Information Needs to Evaluate Whether Bay Ecosystem Health is Adequately Protected. 2-139 3-1. San Diego Bay Tidelands by Ownership (uncorrected for approximately 1490 acres of land and watertransferred from private and state holdings to USFWS, 1999).3-7 3-2. Natural Resource Management Plans and Approval Dates for the San Diego Bay Area. 3-11 3-3. US Navy, US Coast Guard, and US Marine Corps Uses of San Diego Bay by Organization.3-12 3-4. San Diego Bay Port Master Plan Water Use Mapping Definitions, as Seen in Map 3-4.3-16 xv September 2000 34. San Diego Bay Integrated Natural Resources Management Plan 3-5. Boat Traffic Patterns.3-20 3-6. Future Navy Plans for In-water Projects.3-26 3-7. Proposed Capital Improvement Program Projects for Ports Tidelands, 19992008, Pertinent to this INRMP. 3-27 3-8. Uniform Tourist Tax Collections, FYs 19881996, for Cities in San Diego Bay Region. 3-30 3-9. Federal Agencies with Responsibilities for Natural Resources in San Diego Bay.3-33 3-10.State Agencies with Responsibilities for Natural Resources in San Diego Bay.3-35 3-11.Local Agencies with Responsibilities for Natural Resources in San Diego Bay.3-38 3-12.Examples of Marine Impact Mitigations Described for Recent Bay Projects (Based on EIRs, EISs, and EAs). 3-44 4-1. Salt Marsh Mitigation Standards.4-21 4-2. Attributes That Should be Researched to Determine Their Level of Importance, Practicality, and Cost-effectiveness for Use as a Performance Measure. 4-46 4-3. Candidate Enhancement Opportunity Areas.4-48 4-4. In-water Project Preplanning Checklist4-51 4-5. Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection4-53 4-6. State Marine Protection Area Options: Intent, Methods, Examples.4-59 4-7. Sport Fishing Limits on Fish and Invertebrate Species of San Diego Bay (CDFG 1997). 4-80 4-8. Recreational Angler Catch Sampling List of Major Species for Inland Marine San Diego County, 19931998.4-81 4-9. Historic and Current Habitat Acreages in Four Bay Regions. 4-114 5-1. Summary of Existing and Potential Dredging Projects and Disposal Methods since 1988. 5-5 5-2. Provisions of the CCA Relevant to Dredge Disposal. 5-7 5-3. Biological Effects of Various Dredging Methods Available in San Diego Bay.5-12 5-4. Bay Surface Area Occupied by Fixed Structures (Docks, Piers, Wharves) and by Ships and Boats Using TheseSites.5-28 5-5. Quantity and Type of Bay Habitat Surface Covered by Docks, Piers, Wharves, and Docked Ships and Boatsat Maximum Use. 5-29 5-6. Projected Net Gain or Loss in Bay Coverage from Navy Wharves, Piers, and Floating Docks., 5-29 5-7. Totals and Averages for Specific Disturbance Types for the Entire South Bay Study Area. 5-41 5-8. Percentage of Birds Sampled Avoiding Survey Boat by Distance Category in Central San Diego Bay. 5-41 5-9. Federal and State Statutes Affecting Management of Contaminated Sediment. 5-60 5-10.Sample target audiences, implementers, and funding sources for environmental education projects.5-76 5-11.Suggested bird observation locations for public access or long-term monitoring. 5-80 6-1. Priority Monitoring Parameters Agreed Upon by the San Diego Bay Interagency Water Quality Panel. 6-7 6-2. Examples of Proposed Use of Ecological Indicators to Learn about San Diego Bays Condition and Trend6-10 6-3. Priority Long-term Monitoring Parameters. 6-12 6-4. List of Candidate Target Species for Supporting Long-term Monitoring and for Project Planning.1 6-14 6-5. Research (or Pre-research) Interests Identified by TOC (April 21, 1999).6-20 7-1. Existing Institutions to Implement the Plan (TOC Members Noted with *).7-4 7-2. Evaluation of New Organization Options for Plan Implementation.7-5 7-3. Examples of Formal and Informal Institutional Mechanisms for Implementation. 7-6 7-4. Available Primary Funding Sources for Plan Implementation. 7-7 7-5. Ideas for New Funding Sources for Bay Ecosystem Management. 7-11 7-6. First-year Priorities for Resource Manager/Stakeholder Committee and Focus Team Subcommittees.7-14 E-1. San Diego Bay Plant Species and Their Habitats.E-3 E-2. San Diego Bay Invertebrate Species and Their Habitats. E-7 E-3. San Diego Bay Fishes: Their Habitats and Feeding Strategies.E-20 E-4. San Diego Bay Birds: Their Diet, Status, and Habitat. E-25 G-1. Ecological History of San Diego Bay. G-3 xvi September 2000 35. San Diego Bay Integrated Natural Resources Management Plan List of Maps 1-1. San Diego Bay, the Conceptual Watershed Influence Zone, in the Southern California Bight. 1-6 1-2. San Diego Bay INRMP Functional Planning Zone, or Footprint. 1-7 1-3. San Diego Bay INRMP Functional Planning Zone and Conceptual Watershed Influence Zone. 1-8 2-1. Recent Topography of San Diego Bay Floor. 2-5 2-2. Cumulative History of Dredge and Fill Activity in San Diego Bay.2-6 2-3. Percent Fine Sediments (Silt and Clay) on the Bay Floor.2-7 2-4. Half-life of Water residing in the Bay with Varying Tidal Amplitudes, taking into Account mixing of BayWater with Ocean Water during Tidal Cycles. The Data are based on a Two-Dimensional HydrodynamicModel (depth not considered), validated with Salinity and Temperature Correlations. Data and Graphicsprovided by Don Sutton and John Helly of the San Diego Supercomputer Center. Legend on Graph saysHours for 50% dilution.2-11 2-5. San Diego Bay Benthic Community Quality Analysis.2-21 2-6. Salt Marsh and Upland Transition Adjacent to San Diego Bay.2-37 2-7. Shoreline Structures of San Diego Bay. 2-42 2-8. Relative Abundance of Birds Based on Three Surveys Conducted in 19931994. 2-95 2-9. Biodiversity of Birds Based on Three Surveys Conducted in 19931994. 2-96 2-10.Least Tern Foraging and Nesting Areas in San Diego Bay. 2-122 3-1. San Diego Bay Historic Habitat Footprint (1859), with Current Shoreline Overlay.3-4 3-2. San Diego Bay Regional Land Use.3-8 3-3. Local Planning Jurisdictions of San Diego Bay Environs.3-10 3-4. San Diego Bay Port Jurisdiction Master Plan Water Use Designations.3-15 3-5. San Diego Bay Marinas, Docks, and Public Recreational Areas. 3-18 3-6. Boat Traffic Patterns on San Diego Bay (Refer to Table 3-5 for Detailed Explanations of this Map). 3-19 3-7. San Diego Bay Water Navigation Systems and Restricted Areas. 3-22 3-8. San Diego Bay US Naval Facilities and Planned Capital Improvements Summary (19972002).3-25 4-1. Past Mitigation Projects in San Diego Bay. 4-45 4-2. Protected Marine and Coastal Habitat in San Diego Bay1998.4-56 5-1. San Diego Bay Oil Spills Reported to US Coast Guard (19931996). 5-67 5-2. Suggested bird observation points for public viewing or for a long-term monitoring program.5-82 C-1. Habitats of San Diego Bay. C-3 C-2. Mean Numerical Density of All Fish Species January Samples, 19951999. C-5 C-3. Mean Numerical Density of All Fish Species July Samples, 19941998.C-7 C-4. Mean Biomass Density of All Fish Species January Samples, 19951999. C-9 C-5. Mean Biomass Density of All Fish Species July Samples, 19941998. C-11 C-6. Potential Enhancement Sites in San Diego Bay. C-13 xvii September 2000 36. San Diego Bay Integrated Natural Resources Management Plan xviii September 2000 37. San Diego Bay Integrated Natural Resources Management Plan List of Photos 1-1. Aerial Photo of San Diego Bay Region.1-3 1-2. San Diego Bays Urban Shoreline.1-14 2-1. South Bay Mudflat Adjoining Northernmost Levee of Salt Works.2-1 2-2. Sea Lions Napping on Buoy.2-24 2-3. Birds Rafting.2-26 2-4. Ray on soft bottom sediment.2-27 2-5. Eelgrass bed. 2-30 2-6. Small Mudflat Adjacent to Delta Beach, Showing Sediment Churned Up At High Tide. (1998).2-34 2-7. Mudflat of South Bay. 2-35 2-8. Invertebrate in Riprap. 2-43 2-9. Salt Works. 2-46 2-10.Sand Hummocks with Ambrosia Chamissonis.2-48 2-11.Dune Vegetation in Flower.2-49 2-12.Sweetwater Channel. 2-51 2-13.Wandering Sponge (Tetilla mutabilis) with the Ectoprot Zoobotryon verticillatum and Algae, IncludingGracilaria spp. 2-65 2-14.Anemones and Tube-forming Polychaete Worms Living on Man-made Surface (a Sunken Boat).2-67 2-15.Killifish.2-69 2-16.Beldings Savannah Sparrow on Pickleweed.2-129 3-1. San Diego Bay Pier With Downtown in Background.3-1 3-2. Aerial Photos of San Diego Bay 1928. 3-2 3-3. North Island 1936. 3-5 3-4. US Navy Cruiser and Destroyer.3-11 3-5. San Diego Bay.3-14 3-6. Bait for Fishing Available in the Bay.3-23 3-7. City of San Diego.3-26 4-1. Egret at Low Tide. 4-1 4-2. Bay Traffic. 4-3 4-3. Crater Produced by a Tube Worm or Bivalve Mollusk. 4-8 4-4. Eelgrass Bed. 4-12 4-5. Mudflat.4-15 4-6. San Diego Bay Salt Marsh. 4-20 4-7. Black skimmers on Salt Works Levee. 4-31 4-8. Planting Eelgrass.4-38 4-9. Black-necked Stilt. 4-42 4-10.Heron Park Sign at NASNI. 4-52 4-11.Heron.4-88 4-12.Green Sea Turtle. 4-99 4-13.California Least Tern. 4-104 5-1. Coronado Bridge Over San Diego Bay.5-1 5-2. Dredging in San Diego Bay. 5-4 5-3. Sailing on San Diego Bay. 5-26xix September 2000 38. San Diego Bay Integrated Natural Resources Management Plan 5-4. Boat Ramp with Riprap.5-28 5-5. Waterbirds of the Bay.5-35 5-6. Jet Skier with Navy Carrier.5-36 5-7. Waterbirds and Boats on San Diego Bay.5-38 5-8. Riprap Armoring near Coronado Cays. 5-69 6-1. Gull-billed Tern.6-1 7-1. Shells of a San Diego Bay Mudflat. 7-1 xx September 2000 39. San Diego Bay Integrated Natural Resources Management Plan Executive Summary Marinas, submarines, hotels, Navy SEALS, cruise ships, docks, freighters, yachts, air- craft carriers, jet skis, terminals, parks... Harbor seals, black brant, bay gobies, tunicates, brittle stars, mud shrimp, bay mussels, sea pansies, eelgrass, salt marsh birds beak, sargassum... One bay, many values. Can they all thrive?This San Diego Bay Ecosystem Plan is a long-term strategy sponsored by two of the majormanagers of the San Diego Bay: the US Navy and San Diego Unified Port District (SDUPD).Its intent is to provide direction for the good stewardship that natural resources require, while alsosupporting the ability of the Navy and Port to meet their missions and continue functioningwithin the Bay. The ecosystem approach reflected in the Plan looks at the interconnectionsamong all of the natural resources and human uses of the Bay, across ownership and juris-dictional boundaries. San Diego Bay is viewed as an ecosystem rather than as a collection ofindividual species or sites or projects. Ensure the long-term health, recovery The Bay Ecosystem Plans goal is to: and protection of San Diego Baysecosystem in concert with the Bayseconomic, Naval, recreational,navigational, and fisheries needs. 40. San Diego Bay Integrated Natural Resources Management PlanThis Plan is intended to be an agent of change. To this Plan and coordinate projects and activities so thatend, beginning in Chapter 1, the Plans vision for Santhey are compatible with natural resources (ChapterDiego Bay is outlined. The current state of the ecosys- 5);tem is described in Chapters 2 and 3, spelling out the Improve information sharing, coordination andexisting baseline from which managers and users can dissemination (Chapters 5 and 6);measure progress. Chapters 4, 5, and 6 lay out a path-way to change for proceeding toward the Plans goal Conduct research and long-term monitoring thatsupports decision-making (Chapter 6); andand vision. They flesh out a progression not towards thehistorical Bay, because that is gone forever, but towards Put in place a Stakeholders Committee and Focusone that is wilder, with softer shorelines, richer andSubcommittees for collaborative, ecosystem-basedmore abundant in native life. They also describe a Bayproblem-solving in pursuit of the goal and objec-that, while used for thriving urban, commercial, andtives (Chapter 7).military needs, has an increasing proportion of usesthat are passive. It is moving towards a place with more A cooperative effort of many people brought this Planopportunities for public access, recreation, education together. Besides representatives from the Navy andand enjoyment of the myriad benefits of a healthy, SDUPD, regulatory and resource agencies formed thedynamic ecosystem. Finally, the Bays managers and lead umbrella group called the Technical Oversightstakeholders will make sounder decisions because ofCommittee (TOC). Representatives from nonprofit orga-positive collaboration among themselves, a clearer nizations and the environmental community also par-understanding of the cumulative effects of their ticipated in this diverse group of 13 organizations,actions, and information support from focused research represented by 18 individuals. The TOC members vary-and long-term monitoring. The Plan contains over ing perspectives helped ensure that ecosystem manage-1,000 strategies for better management of the Bay. Taskment strategies were considered in institutional, social,forces, committees, partnerships, cooperative agree- and economic contexts to validate the Plans ecosystemments, memoranda of understanding, monitoringapproach. Another advisory committee was the Navystrategies, research projects, award programs, informa-Installation Oversight Committee (NIOC), composed oftion exchange mechanisms and endowment funds are representatives from each of the major Navy installa-among the strategies described.tions around the Bay as well as from the US Coast Guard (USCG) and Cabrillo National Monument. UniversityThe core strategies are to:and consultant scientists were asked to participate on Manage and restore habitats, populations, and eco- the Science Advisory and Review Team. Their role was to system processes (Chapter 4); help develop the scientific basis of the Plan. Public com- xxiiSeptember 2000 41. San Diego Bay Integrated Natural Resources Management Plan ment by those interests not represented on any of theremains has been modified by structures for shore- committees was actively sought. Public workshops wereline stabilization or access. The Plan seeks to set tar- sponsored by the TOC in July 1997, July 1998, and Sep- gets for support of sensitive or declining species in tember 1999. Verbal and written comments helpedthis habitat, such as the western snowy plover, forag- identify new data sources, important issues for the Plan,ing California least tern, shorebirds, and juvenile and some recommendations on strategy.California halibut. Intertidal enhancement projects Several related, regional efforts have gone on concur- using dredge material are a top priority. rently with this Plan. The San Diego Bay Interagency The Plan seeks an improvement in the habitat valueWater Quality Panel of developed shorelines and marine structures and(SDBIWQP or Baytheir functional contribution to the ecosystem. NewPanel) met for fiveshoreline stabilization structures should be mini-years to develop amized, and existing structures should be enhancedComprehensive Man-as habitat for fish and wildlife. When new armoringagement Plan for Sanor reconstruction of degraded armoring is demon-Diego Bay (SDBIWQPstrably unavoidable, it should be designed to incor-1998). Water qualityporate maximum practical habitat value for nativeissues were the mainspecies, giving priority to solutions that use materi-focus of this effort, but als of the type indigenous to the Bay. There shoulda range of naturalbe a means to provide incentive for habitat enhance- resource, wildlife, and human use issues were also ment of existing shoreline stabilization structures, addressed. On related issues, this Bay Ecosystem Planwhich currently vary greatly in their ability to sup- incorporates many of the recommendations of the Bayport native species. Panel; however, the intent is not to overlap with water A San Diego Bay Shoreline Stabilization and Resto- quality regulatory issues. ration Plan should be developed that involvesSDUPD, US Navy, regulators and resource agencies. Key Findings and StrategiesThe Plan should set goals for protecting and enhanc-ing natural shoreline functions, prevent new shore- Habitats and Populationsline impacts, restore shoreline functions as The shallower habitats and the Bays natural shoreline redevelopment occurs, arrest erosion and accretion have been severely depleted or modified. Compared to problems around the Bay, and allow regulators to historic acreages, there has been a 70% loss of salt marsh,view the Bay as a whole system, rather than piece- 84% loss of intertidal areas other than salt marsh, and ameal. The Plan should provide techniques for add- 42% loss of shallow subtidal areas. In contrast, deep watering habitat value to structures as they need to be habitat has doubled since the Bays first dredging in 1914.replaced, and identify means to provide economic Also, 74% of the shoreline is now armored with artificialincentive to improving the habitat value of existing hard structures, a type of substrate not native to the Bay.structures. Upland transition areas needed by many species are now Moderately-deep subtidal habitat should be tar- scarce and converted to urban uses.geted for potential habitat enhancement by convert- Habitats ing to shallower depths A formal policy for protection of unvegetated shal-that are more produc-lows, intertidal flats, and upland transition areas tive due to enhancedshould be adopted by the resource and regulatorylight penetration. Appro-agencies because current protection is considered priate preplanninginadequate. A draft policy is in Appendix H.should be conducted totake advantage of oppor- The Plan allows for no net loss of shallow subtidaltunities for filling mod-habitat in acreage or in existing biological functionserately-deep habitats toand values, and seeks long-term enhancement of eel-shallow or intertidal ele-grass habitat. Continued enforcement of mitigationvations.standards under the Southern California EelgrassMitigation Policy is necessary. Salt marsh acreageshould be expanded and This Plan seeks a long-term net gain of area, func-enhanced, as should thetion, value and permanence of intertidal flats, andlinkages between saltthe physical conditions which support this habitat.marsh and other habitats.Intertidal habitat encompasses the area betweenSome priority sites forhigh and low tides. Losses in this zone have been theenhancement include themost severe of all Bay habitats, and most of whatnorth end of D-Street,xxiii September 2000 42. San Diego Bay Integrated Natural Resources Management Plannorth side of Gunpowder Point, E-Street marsh on themented. The ecological functioning of the Otay Riversouth side of Gunpowder Point, J-Street Marsh, the100-year floodplain should be restored.South Bay Marine Biological Study Area, and Emory Creation of new deep-water environments by dredg-Cove. Greater setbacks that effectively protect habi- ing should be minimized, while protecting the func-tat values should be required in California Coastal tions these habitats provide. These functions includeCommission (CCC) permits for new construction,the transport of plankton into and out of the Bay forespecially for sensitive habitats such as the saltcoastal species (such as the larvae of many fishes andmarsh.crustaceans) that depend on access to the warm, Uplands which border the Bay are important as a sheltered, shallow waters during early life cycle buffer between the natural and constructed stages. Consideration should be given to keeping environment, and for the large numbernew navigation channels to the east side of the Bay,and diversity of birds that require them. where they are currently aligned. Some unused navi- In these transition areas, appropriate gation channels could be enhanced to benefit fishlandscaping designs (bayscaping)and wildlife by shoring them up to shallower, more should be encouraged. Bayscaping uses aproductive depths for these species, and some could minimum of pesticides and fertilizers on proper- be realigned for enhancement purposes.ties within a vegetation management corridor alongthe Bays shoreline to enhance habitat value, preventpollution, conserve water, and control exotic intro-ductions. A demonstration brochure should be dis- Populationstributed, and an award system should be promoted This Plan places a high priority on the long-termthat recognizes the best use of appropriate landscape protection and monitoring of both plant planktondesigns. High priority enhancement sites in the and zooplankton. Zooplankton include the eggs andupland transition are vacant parcels along the south- larvae of fish and crustaceans that need to drift intowest shore such as: Emory Reserve, South Bayshallow or intertidal Bay waters from the open oceanMarine Biological Study Area, and the parcel leased to complete their juvenile life stages.by the US Navy to California Department of Parksand Recreation until that lease expires. Algae that indicate pollution should be minimized,while algal mats in otherwise unvegetated shallows The salt ponds at the south end of the Bay should beadd structure to the habitat and shouldanalyzed for an optimal arrangement and combina-be protected.tion of salt marsh, tidal flat, salt pond, and dike habi-tats. Consideration should be given to enhancing the Protection of invertebrate commu-interconnection between the salt ponds and nearby nities should be founded on pro-mudflat and salt marsh habitat. The nature of the salttecting the substrate and water qualityextraction process has facilitated use of this artificial upon which they depend. Inverte-habitat by many shorebirds, seabirds, and waterfowl.brates should be monitored for their safety forIt represents one of the few large feeding, roosting, and human consumption through studies that assess thenesting areas remaining along the urbanized southerneffects of toxics and their severity.California coast. Enhancement should be targeted for San Diego Bays function as a crucial nursery and ref-shorebird foraging, seabird nesting, and endangered uge for marine fishes, including those that live else-or threatened species support.where as adults, requires protection and The function and values of river and stream mouthsenhancement. The warm water temperatures andas natural corridors and buffers between salt water high productivity during the spring and summerand freshwater habitats should be examined andmonths in shallow and intertidal waters enable theenhanced to more nearly approach their natural role.Bay to support large numbers of larval and juvenileToday, streams draining into the Bay are channelizedfishes. Many of these abundant fishes are important or confined to storm drains and sometimes com- forage for fishes of commercial or sport fishing value pletely missing. Stormwater outfalls provide and for seabirds. The Bay also supports large numbers some flows and nutrients to the Bay, but not of fish eggs and larvae in planktonic form. Another with natural seasonality, timing, fre- important characteristic of the fishes inhabiting San quency, or content. Opportunities to Diego Bay is that they form unique species assem- replace the corridor, buffer, filtering, and blages not found outside of southern California, andepisodic siltation function formerly played bythus contribute to the biodiversity of fish populations.uncontrolled streams should be identified and imple- This Plan targets an increase in the Bays carryingcapacity for shorebirds, nesting seabirds, and marshand upland transition resident birds. It advocatesestablishing specific population targets for priority xxiv September 2000 43. San Diego Bay Integrated Natural Resources Management Planbird populations and to secure and conduct the nec- the Bay as defined by state, federal, and other organi-essary management, enhancement, or expansion of zational lists.habitat to support those targets. This Plan seeks enhanced protection of the local for-San Diego Bay provides the largest expanse of pro-aging population of the green sea turtle.tected Bay waters in southern California for migra- An increase in fledgling productivity and pair numberstory birds on the Pacific Flyway. More than 305 birdof the California least tern is sought, in part by adopt-species have been documented using the Bay. The ing a Baywide approach to predator management.majority of Bay birds, representing 30 families, areOther management activities for the protection ofmigratory and rely on the Bay as an important rest-sensitive species are habitat-based, as described above.ing and feeding stopover. Others, especially thosearriving from tropical latitudes, spend the winter,Compatible Use of the Bays Natural Resourcesbreed or nest. One-third of birds dependent on SanDiego Bay have been identified as sensitive or declin-Mitigation and Enhancementing by the federal or state governments or by the An improvement is sought in the effectiveness and successAudubon Society.of mitigation and enhancement projects by building a Secure nesting sites for colonial seabirds should be consensus of prioritized need among regulators andprovided that allow for project proponents.population recovery bymanaging predators andenhancing habitat. Coop-erative agreements onpredator management thatresult in more effectiveprotection of nesting birds should be put in place. Aggressive avoidance should remain the primary This Plan seeks to head off the invasion and prolifer- strategy to avoid loss of natural resource functionsation of exotic species as a serious threat to the integ- and values in the Bay.rity of the ecosystem. At least 82 nonindigenous The use of dredge material for beneficial reuse in thespecies are found in the Bays planning zone. Bay should be maximized, consistent with the habitatBallast water controls are necessary. The USCGobjectives and policies of this Plan and other compre-should be supported in its effort to begin sampling hensive, regional planning efforts. A multiuser benefi-ships and to promulgate mandatory regulations ascial reuse site for habitat restoration or enhancementnecessary. The Navys ballast water exchange policy in the Bay should be identified so that project sponsorsfor open-ocean exchange should continue, and thefrom multiple jurisdictions may contribute jointly toimplementation of a ballast water management pro- an enhancement project over time and as dredge mate-gram that explicitly addresses the nonindigenousrial accumulates.invasive species problem is encouraged. DredgingThe number of new invasive exotic species should be When dredging is necessary it should be conducted in anreduced or prevented by educational and preventiveenvironmentally sound manner.methods. For example, appropriate landscaping andrestoration practices that control the introduction of Ecosystem processes, habitat values and species thatinvasive exotic plants are encouraged.are affected by dredging should be documented anddescribed in sufficient detail to ensure adequate mit-The City of San Diego should designate the Bay as igation. For example, at intertidal sites the habitatopen space for the purposes of its Biological Mitiga- functions and values for fishes, invertebrates andtion Ordinance, prohibiting the use of invasive exoticshorebirds should be detailed so that all areplants near a designated open space area. addressed and protected.A San Diego Bay Exotic Species Task Force should be Dredging should be first avoided, then minimizedformed which is composed of resource managers,close to shore, in order not to contribute to furtherresearchers and interested public to implement theloss of intertidal habitats and the need to armor theabove strategy. The Task Force should oversee anshoreline. Prioritize new dredging at locations whereExotic Species Control Endowment Fund.the shoreline is already armored. Maximize use of Support of seven species federally listed as threat- existing channels rather than creating new ones.ened or endangered that occur within the Bay Eco- New locations for both upland and nearshore con-system Plan footprint is an important Bay function. fined disposal sites should be investigated. Seek aMany other sensitive species occur in and aroundmeans to combine habitat enhancement with near-shore confined disposal sites. xxv September 2000 44. San Diego Bay Integrated Natural Resources Management PlanRecreational Harvestinghabitat disturbance should be taken to protect sensi-Harvest management is targeted to support viable, self-sus-tive bird populations.taining populations and promote native species richness. SDUPDs Boaters Guide should be expanded to include avoidance of surface bird use, as well as eel- More effective measurement of all types of recre- grass, green sea turtle areas, and marshes.ational harvesting within the Bay should be pro-moted. Examples are: 1) to expand periodic censusing Any effects of lighting and other disturbance should(e.g. boat and dock checks) of all species; 2) increasebe minimized by establishing setbacks for new con-censusing of California halibut and sand bass; struction and other strategies near important nesting3) require that data collectors keep separate data for and roosting sites. The CCC should increase its set-the San Diego Bay sport fishery so that their catchesback requirements near marshes.can be considered separately from those in the ocean;Ecotourismand 4) encourage a bait fishery monitoring program, The potential for ecotourism development related tosuch as for ghost shrimp. To accomplish this, stable birdwatching should be pursued, and use of publicrevenue sources to supplement license revenues for lands for this purpose encouraged in a manner con-the California Department of Fish and Games sistent with maintaining local resource values.(CDFG) enforcement efforts are sought. Water and Sediment Quality ManagementShip and Boat Maintenance This Plan seeks to reduce and minimize harmful stormwa-Water and sediment quality are targeted for improvement ter pollutants from entering the Bay from watershed users.with improved ship and boat maintenance practices. The San Diego Bay Watershed Task Force should be Marina operators are encouraged to use Best Man- encouraged to develop a pilot program aimed at solv-agement Practices (BMPs) that are beyond the mini- ing contamination of the Bay from runoff. The exist-mum practices often expected, such as: 1) adding ing Municipal Stormwater Education Committeegreen vegetated buffers at marina sites where possi- should be a core group of the Task Force. The Taskble to filter runoff into the Bay, and 2) moving power Force should develop watershed problem and needwash pads for boat hulls away from the bulkhead assessments, as well as identify and implement BMPs.and adding filters to capture paint chips. Baseline contaminant levels in selected San Diego Pollution prevention is a major priority for boatyards Bay seafood species should be established, so thatand shipyards. Support improved practices at boat- changes over time can be detected in support of pro-yards and shipyards by recognizing significant efforts tecting the public from health risks associated withthrough an annual Better Bay Award program. consuming seafood. A field demonstration/pilot project of promising non- Fish and wildlife should be monitored for and pro-toxic coatings on ships and boats in San Diego Bay tected from contaminants.should be promoted to help evaluate the coatingseffectiveness in terms of durability, bonding and repel- Cumulative Effectslency of fouling organisms under local conditions. The format by which cumulative effects are discussed inSurface Water Useenvironmental documentation should be standardized so that they can be better evaluated, avoided, and minimized.The various surface uses of the Bay by watercraft need to beproperly balanced with conservation priorities for water- A format is proposed in this Plan. It includes stan-and shorebirds.dardized and multiple scales of analysis, and an information clearinghouse on local extirpations or The Plan advocates seasonal restrictions for water-declines of species at risk. Project areas should becraft in priority bird-use areas. Practical steps, such as properly identified and bounded such that all otherwatercraft speed reduction, noise and light reduction projects that overlap in time and space with a projector shielding, and avoidance of bird assemblages and area boundary are considered. The target management species identified in this Plan should be used to help focus the analysis of potential impacts. xxviSeptember 2000 45. San Diego Bay Integrated Natural Resources Management Plan Environmental Education A biannual report on the State of San Diego Bay Education of the public is one of the highest priorities of should be produced with the results and synopses of the Plan, because only an aware public can ensure that thelong-term monitoring and ongoing research. It most necessary steps are taken to protect the Bay.should be presented in a manner useful to managers and the public. Development of educational partnerships amongnonprofit organizations, government, schools, and Target management species should be selected for long-term or periodic monitoring to provide a focusbusinesses that focus on the Bay are encouraged. for management activities. Certain species are iden-Workshops, seminars, literature, a web page, inter- tified to help focus planning, management, moni-pretive signs, wildlife observation decks and board- toring and research that represent particularwalks are proposed. habitats, processes, interdependencies or vulnerabil- A community-based restoration project should be ities in the Bay. Examples are juvenile California hal-implemented, using as a model the ongoing successibut, light-footed clapper rail, and black brant.of the Paradise Creek project. Both public and private jurisdictions should imple- Long-term funding should be put in place to ensure thement monitoring,continuance of environmental education programsincluding a citizen-about San Diego Bay. Explore use of a bed-tax from based program tovisitors hotel tax as a source of interpretation funds. help plug gaps in The Ecosystem as a Functional Whole coverage. This Plan adopts an ecosystem approach to managing nat- A committee ural resources in two primary ways: should be established to make deci- 1. Planning, management, monitoring, and research sions on long-termare proposed at several hierarchical scales and time monitoring, priorities, phasing or stepwise imple-frames that are biologically meaningful, such as mentation of monitoring elements, quality assur-whole-Bay, Bay subregion, habitat, and site scales. ance and quality control, and effectiveThe Plan also encourages that necessary changes dissemination of monitoring results to a broad audi-occur beyond its current footprint such as up the ence. This committee will not make managementwatershed, and in conjunction and communication recommendations.with surrounding systems such as Mission Bay,Tijuana Estuary, Los Penasquitos Lagoon, and others. Research Program 2. Ecosystem components are viewed not just as iso- This plan seeks improved targeting of research to supportlated elements, but as interdependent components management objectives and decision-making.linked by food web, nutrient cycling, and other pro-cesses. For example, the ecological indicators pro- A means to prioritize research projects is proposedposed to act as management cues represent both that involves a Priority Problem List and the rankingparts of the ecosystem and the processes that link of management objectives.these parts. A committee of scientists, managers, landowners and users, and the involved public is needed to pri- Long-term Monitoringoritize research needs. The purpose of the Research A long-term monitoring program is a key element of theCommittee will be to set research priorities in rela- Bay Ecosystem Plans strategies for better Bay manage-tion to management concerns, decide what management. The primary objectives of such a program are to ment concerns make a Priority Problem List and detect ecological trends and determine their cause. ranking of issues on the list, assure the quality of research conducted and tie-in to management, and Indicators, or markers, of ecological health are iden- to communicate research results effectively to atified for long-term monitoring. They are intended broad audience.to provide cues for adaptively managing the Baysnatural resources. These include monitoring a core Project-related research and monitoring canset of elements, such as the physical and chemical enhance learning and experience, such as to bettercharacteristics of the water column and sediment,define the area affected by a project and cumulativechlorophyll, habitat quantity or quality change, effects, the strength of dependencies among habitatschanges in land use both around the Bay and in the and organisms (productivity, physical material trans-upper watershed, and changes in populations such port, tidal circulation, biological linkages such asas zooplankton, invertebrates, exotics, algae, vegeta- migration and feeding dependencies, etc.).tion, fishes, birds, and marine mammals.xxvii September 2000 46. San Diego Bay Integrated Natural Resources Management Plan Standardized and cost-effective protocols should bePlanning and Coordinating Projectsused to encourage reliable comparisons amongand Activitiesprojects, and between short- and long-term monitor- By virtue of its comprehensive, interagency, and interdis-ing programs. ciplinary approach, this Plan accomplishes one of its pri- Experimentation and implementation of alternativemary purposes--to be an effective tool for project plannersshoreline and underwater habitat structures that areand Bay managers.more beneficial to the environment should be facili-tated. If shown to be environmentally safe, durable,Tools for Accomplishing the Plans Goalstrong and cost-effective, a replacement program forand Objectivesall chemically-treated wood pilings with plastics It is the desire of everyone who worked long and hard onwithin the Bay should be promoted. A high prioritythis Plan that it be successful.for experimental use of plastic pilings may be areas A new Stakeholders Committee and Focus Subcom-designated as Polynuclear Aromatic Hydrocarbons mittees to lead Plan implementation are proposed.(PAHs) hot spots. A first-year program of implementable items to kick Information Sharingoff Plan implementation are presented in Chapter 7. To improve the effective and efficient allocation of A number of new cooperative agreements, task resources, information on the Bay should be well-orga- forces, committees, endowment funds, and joint nized and accessible.memoranda are proposed, with roles for agency,public, private, and nonprofit organizations. A central clearinghouse should be set up for data,reports and publications on the Bays naturalresources that is accessible to a broad range of users,both technical and nontechnical. The criteria forselection of an institution for managing a data clear-inghouse should include: longevity, objectivity, abil-ity to work with the public, and cost-benefit. Events are needed to promote data sharing, technol-ogy transfer, and communication for a broad rangeof involved parties, including a newsletter to reporton progress in implementing this Plan and other Bayactivities, biannual reporting on the State of SanDiego Bay, workshops and conferences, and cross-disciplinary field programs. xxviiiSeptember 2000 47. San Diego Bay Integrated Natural Resources Management Plan Part I: Introduction 48. San Diego Bay Integrated Natural Resources Management Plan 1.0Welcome to the PlanThis Port of San Diego is beautiful to behold,and does not belie its reputation. Father Serra, 1769 1.1 The Plan: Why, What, and WhereMarinas, submarines, hotels, Navy SEALS, cruise ships, docks, freighters, yachts, air-craft carriers, jetboats, terminals, parks...Harbor seals, black brant, bay gobies, tunicates, brittle stars, mud shrimp, bay mussels,sea pansies, eelgrass, salt marsh birds beak, sargassum...Photo 1999 Peg Spencer.One Bay, many values. Can they all thrive?This San Diego Bay Integrated Natural Resources Management Plan is a long-termstrategy for two of the major managers of the Bay: the US Navy and the San DiegoUnified Port District (SDUPD). Its intent is to provide direction for the good steward-ship that natural resources require, while also to support the ability of the Navy andthe Port to meet their missions and continue functioning within the Bay. September 2000 49. San Diego Bay Integrated Natural Resources Management PlanA new approach reflected in the Plan is to look at the interconnections among allof the natural resources and human uses of the Bay, across ownership and jurisdic-tional boundaries. San Diego Bay is viewed as an ecosystem with all of its processesrather than as a collection of individual species or sites or projects. As such, thisPlan was nicknamed the Bay Ecosystem Plan.This Plan is intended to be an agent of change. To this end, many new strategiesand tactics for Bay managers are proposed. These include new, or changes inexisting, policies for:protecting Bay habitats and ecological processes;planning for current and future uses, including for mitigation and enhancement, and analyzing for cumulative effects; anddeveloping a research and long-term monitoring program to support decision-making. 1.1.1 The Plans GoalA Goal Statement is an essential component of a successful plan. Goal is definedhere as a broad statement of intent, direction and purpose; an enduring, visionarydescription of where you want to go. A goal is not necessarily completely obtainable.However, its vision is used as the compass of a plans progress: are we continuing tomove in the agreed upon direction? Without the compass, a plan can easily wan-der off course. GoalEnsure the long-term health, recovery, and protection ofSan Diego Bays ecosystem in concert with the Bays economic,Naval, recreational, navigational, and fisheries needs.Habitat conservation and restoration are implied in the first part of the GoalStatement, as well as protection of ecosystem processes that depend on thesehabitats, such as productivity, nutrient cycling, and support of a complex foodweb. These habitats and related processes are specifically addressed in objectivesand strategies in later chapters. 1.1.2 Plan OriginBeginning in 1992, biologists within the Navys Southwest Division office, as wellas from the US Fish and Wildlife Service (USFWS) and the National Marine Fisher-ies Service (NMFS), observed that project-by-project management o

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