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San Diego Bay Integrated Natural Resources Management Plan

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The Port regularly sponsors studies to evaluate eelgrass restoration techniques in San Diego Bay. Assistant Professors and graduate students from San Diego State University conducted a study on the …

The Port regularly sponsors studies to evaluate eelgrass restoration techniques in San Diego Bay. Assistant Professors and graduate students from San Diego State University conducted a study on the effects of habitat structure on fish recruitment and species diversity in eelgrass beds. The project also studied the effects on species density and diversity in native eelgrass beds and where eelgrass has been harvested. Through this study, the Port was seeking knowledge regarding the most effective planting and harvesting schemes that would provide the best results for the bay's ecosystem.

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  • 1. San Diego Bay Integrated Natural Resources Management Plan Public Draft—September 1999 September 8, 1999
  • 2. San Diego Bay Integrated Natural Resources Management Plan Public Draft Coastal America Logo Reference: U.S. Department of the Navy, Southwest Division (USDoN, SWDIV). 1999. San Diego Bay Integrated Natural 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; Natural Resources 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 1997–1999 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 Game Bill Tippets California Department of Fish and Game Marilyn 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 Engineers David 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 Consultant Elizabeth Copper CSU Northridge Larry 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 Island Jan Larson Naval Command Center Operations Specialist Don Lydy Naval Station 32nd Street Mary Ann Flanagan National Park Service, Cabrillo National Monument Carol Knipper US Coast Guard Maritime Safety LT M.T. Cunningham iii September 8, 1999
  • 4. San Diego Bay Integrated Natural Resources Management Plan Public Draft This plan was prepared by: Project Manager Planner-In-Charge Marine Biologist Research, GIS, and Layout and Design Wildlife Illustration Tierra Data Systems Sommarstrom and Assoc. Richard Ford, Ph.D. Editing Catherine Lush Peter Else Elizabeth M. Kellogg Sari Sommarstrom, Ph.D. Department of Biology Cynthia Booth 208 O’Keefe Street 403 South 8th Street 10110 W. Lilac Rd. P.O. Box 719 S.D.S.U. Danielle Booth Menlo Park, CA 94025 Laramie, WY 82070 Escondido, CA 92026 Etna, CA 96027 5500 Campanile Drive Sherman Jones (650) 327-9201 (307) 755-1837 (760) 749-2247 (530) 467-5783 San Diego, CA 92182 James L. Kellogg fax (650) 327-9224 fax (760) 751-9707 Peter McDonald Keri Salmon Scott 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 Plan Approving Officials: Commander, Naval Bases San Diego Date Chair, Board of Port Commissioners Date San Diego Unified Port District Field Supervisor Date Carlsbad Field Office U.S. Fish and Wildlife Service Regional Director Date Region V California Department of Fish and Game v 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 Draft Table of Contents Executive Summary Part I: Introduction 1.0 Welcome to the Plan 1-1 1.1 The Plan: Why, What, and Where 1-1 1.1.1 The Plan’s Goal 1-2 1.1.2 Plan Origin 1-2 1.1.3 Purpose 1-5 1.1.4 Planning Zones 1-6 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 Plans 1-15 1.2 San Diego Bay: An Important and Sensitive Resource 1-16 1.2.1 Values 1-16 1.2.2 Key Management Issues 1-17 1.3 Ecosystem Management Framework 1-18 1.3.1 Defining Ecosystem Management 1-18 1.4 Strategic Design of Plan 1-19 1.4.1 Audience 1-19 1.4.2 Intent of Use 1-20 1.4.3 Organization 1-20 1.4.4 Implementation 1-21 1.4.5 Updating 1-22 Part II: State of the Bay 2.0 State of the Bay—Ecosystem Resources 2-1 2.1 Ecoregional Setting 2-2 2.2 Physical Conditions 2-2 2.2.1 Climate and Hydrography 2-2 2.2.2 Sediment 2-4 2.2.3 Water 2-11 2.2.3.1 Turbidity 2-11 2.2.3.2 Circulation, Temperature, and Salinity 2-11 2.2.3.3 Residence Time of Water 2-12 2.2.3.4 Hydrodynamic Regions of the Bay 2-15 2.3 Water and Sediment Quality 2-15 2.3.1 Historical Conditions 2-15 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 Draft 2.3.3 Regional Comparisons 2-22 2.3.4 Ecological Effects 2-22 2.4 Bay Habitats 2-24 2.4.1 Deep Subtidal (>–20 ft/–6 m MLLW) 2-28 2.4.2 Moderately Deep Subtidal (–12 to –20 ft (–4 to –6 m) MLLW) 2-29 2.4.3 Shallow Subtidal (–2.2 to –12 ft [–0.7 to –4 m] MLLW) 2-30 2.4.3.1 Unvegetated Shallow Soft-Bottom 2-31 2.4.3.2 Vegetated Shallow Subtidal 2-33 2.4.4 Intertidal (+7.8 to –2.2 ft [+2.4 to –0.7 m] MLLW) 2-35 2.4.4.1 Intertidal Flats 2-36 2.4.4.2 Salt Marsh 2-39 2.4.4.3 Artificial Hard Substrate 2-46 2.4.5 Salt Works 2-51 2.4.6 Upland Transitions 2-52 2.4.6.1 Beaches and Dunes 2-52 2.4.6.2 Coastal Created Lands and Disturbed Uplands 2-55 2.4.6.3 Freshwater Wetlands and Riparian 2-56 2.4.6.4 River Mouths 2-57 2.5 Species Assemblages 2-58 2.5.1 Plankton 2-58 2.5.1.1 Phytoplankton 2-59 2.5.1.2 Zooplankton 2-60 2.5.1.3 Ichthyoplankton 2-61 2.5.2 Algae 2-64 2.5.2.1 Macroalgae 2-64 2.5.3 Invertebrates 2-66 2.5.3.1 Invertebrates of Soft Bottom, Unconsolidated Sediment 2-67 2.5.3.2 Invertebrates of Eelgrass Beds 2-71 2.5.3.3 Invertebrates of Man-made Habitats 2-72 2.5.3.4 Assessment of Invertebrates as Indicators of Pollution or Habitat Disturbance 2-73 2.5.4 Fishes 2-75 2.5.4.1 Description 2-75 2.5.4.2 Species Composition Baywide 2-78 2.5.4.3 Rankings Based on Ecological Index 2-78 2.5.4.4 Comparison of Total Abundance and Biomass Among Bay Regions and Habitats 2-79 2.5.4.5 Comparisons of Abundance by Region 2-79 2.5.4.6 Seasonal Changes in Abundance and Biomass 2-81 2.5.4.7 Patterns of Biodiversity and Species Assemblages in Four Regions of the Bay 2-82 2.5.4.8 Functional Groups of Fishes 2-83 2.5.4.9 Species Caught by Commercial or Recreational Fishing 2-92 2.5.4.10 Warm Water Species in San Diego Bay During El Niño Conditions 2-92 2.5.4.11 Correlation of Fish Abundance With Environmental Factors 2-93 2.5.4.12 Possible Sensitive Habitats or Nursery Area for Fish in San Diego Bay 2-94 2.5.5 Birds 2-94 2.5.6 Marine Mammals 2-109 2.5.6.1 Mammals of Interest 2-110 2.5.6.2 Historical Changes in the Bay 2-110 2.5.6.3 Ecological Roles in the Bay 2-111 2.5.6.4 Species Accounts 2-111 2.5.7 Exotic Marine and Coastal Species 2-113 2.5.7.1 History and Background 2-114 2.5.7.2 Species of Interest 2-115 2.5.7.3 Sources of Marine and Coastal Exotics 2-119 2.5.7.4 Ecological and Economic Impacts 2-119 2.5.7.5 Potential Invasions of Exotics to San Diego Bay 2-121 viii September 8, 1999
  • 9. San Diego Bay Integrated Natural Resources Management Plan Public Draft 2.6 Sensitive Species 2-122 2.6.1 Federally Listed Species 2-123 2.6.1.1 Green Sea Turtle—Chelonia mydas 2-123 2.6.1.2 California least tern—Sterna antilarium browni 2-125 2.6.1.3 Light-footed clapper rail—Rallus longirostris levipes 2-130 2.6.1.4 California brown pelican—Pelecanus occidentalis 2-131 2.6.1.5 Western snowy plover—Charadrius alexandrinus nivosus 2-131 2.6.1.6 Sand dune tiger beetle—Cicindela latesignata latesignata 2-132 2.6.1.7 Salt marsh bird’s beak—Cordylanthus maritimus maritimus 2-132 2.6.2 State Listed Species and Species of Concern 2-133 2.7 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 Webs 2-139 2.7.3.4 Biodiversity 2-141 2.7.4 Disturbance Regimes and Time Scales of Change 2-141 2.8 State of Ecosystem Health: Information Needs Assessment 2-142 2.8.1 What We Need to Know to Describe Bay Ecosystem Health 2-143 2.8.2 What We Currently Understand About Bay Ecosystem Health 2-145 3.0 State of the Bay—Human Use 3-1 3.1 Ecological History of Human Use 3-3 3.1.1 Summary of Human Use and Change 3-3 3.2 The Bay Region’s Human Setting 3-7 3.2.1 Area and Population 3-7 3.2.2 Land Use and Ownership 3-8 3.2.2.1 Bay Water and Tidelands 3-8 3.3 Current Patterns of Use 3-11 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 Navigation 3-20 3.3.6 Fisheries 3-20 3.4 Future Patterns and Plans at the Bay 3-32 3.4.1 Navy 3-32 3.4.2 Port 3-33 3.4.3 City Plans 3-34 3.5 Economics of Use 3-37 3.5.1 Navy 3-37 3.5.2 Port 3-38 3.5.3 Fisheries 3-38 3.5.4 Recreation and Tourism 3-38 3.5.5 Other Uses 3-39 3.6 Overview of Government Regulation of Bay Activities 3-39 3.6.1 Introduction 3-39 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 CEQA 3-48 ix September 8, 1999
  • 10. San Diego Bay Integrated Natural Resources Management Plan Public Draft Part III: Management Strategies 4.0 Ecosystem Management Strategies 4-1 4.1 San Diego Bay’s Natural Resource Values and Ecosystem Management 4-2 4.2 Habitat Protection and Management 4-2 4.2.1 Strategy by Habitat 4-2 4.2.1.1 Deep Subtidal 4-2 4.2.1.2 Moderately Deep Subtidal 4-6 4.2.1.3 Unvegetated Shallow Subtidal 4-7 4.2.1.4 Vegetated Shallow Subtidal 4-11 4.2.1.5 Intertidal Mudflats and Sand Flats 4-14 4.2.1.6 Salt Marsh 4-20 4.2.1.7 Shoreline and Marine Structures 4-25 4.2.1.8 Salt Works 4-31 4.2.1.9 Upland Transition 4-34 4.2.1.10 River Mouths and Floodplains 4-36 4.2.2 Mitigation and Enhancement 4-38 4.2.3 Protected Sites 4-52 4.3 Species Population Protection and Management 4-62 4.3.1 Exotic Species 4-62 4.3.2 Plankton 4-72 4.3.2.1 Benthic Algae 4-74 4.3.2.2 Invertebrates 4-75 4.3.3 Fishes 4-77 4.3.3.1 Harvest Management 4-79 4.3.3.2 Artificial Propagation 4-85 4.3.4 Birds 4-89 4.3.5 Marine Mammals 4-96 4.3.6 Sensitive Species Special Protections 4-100 4.3.6.1 Green Sea Turtle 4-100 4.3.6.2 California Least Tern 4-105 4.3.6.3 Light-footed Clapper Rail 4-108 4.3.6.4 Western Snowy Plover 4-109 4.3.6.5 Salt Marsh Bird’s Beak 4-110 4.4 Ecosystem Approach 4-112 5.0 Compatible Use Strategies 5-1 5.1 Within Bay Project Strategies 5-2 5.1.1 Dredge and Fill Projects 5-2 5.1.2 Ship and Boat Maintenance and Operations 5-17 5.1.3 Shoreline Construction 5-26 5.1.4 Water Surface Use and Shoreline Disturbances 5-34 5.2 Watershed Management Strategies 5-42 5.2.1 The Watershed Management Approach 5-42 5.2.2 Stormwater Management 5-45 5.2.3 Freshwater Inflow Management 5-52 5.3 Cleanup of Bay Use Impacts 5-55 5.3.1 Remediation of Contaminated Bay Sediments 5-55 5.3.2 Oil Spill or Hazardous Substance Prevention and CleanUp 5-62 5.4 Cumulative Effects 5-66 5.5 Environmental Education 5-69 6.0 Monitoring and Research 6-1 6.1 Concepts and Models for Monitoring and Research 6-2 6.1.1 Tenets for Design of a Monitoring and Research Program 6-2 6.1.2 Key Management Questions 6-3 6.2 Program Elements 6-4 x September 8, 1999
  • 11. San Diego Bay Integrated Natural Resources Management Plan Public Draft 6.2.1 Long-term Monitoring for the Bay’s Ecological Condition and Trend 6-5 6.2.2 Project Monitoring 6-16 6.2.3 Research to Support Management Needs 6-19 6.3 Data Integration, Access, and Reporting 6-23 7.0 Implementation Strategies 7-1 7.1 Achieving Success 7-1 7.2 Components of Implementation 7-3 7.2.1 Institutional Resources 7-3 7.2.1.1 Existing Organizations 7-3 7.2.1.2 Potential New Institutions 7-4 7.2.1.3 Mechanisms 7-4 7.2.2 Funding Resources 7-6 7.2.2.1 Existing Sources 7-7 7.2.2.2 Potential New Sources 7-11 7.2.2.3 Volunteer Contributions 7-11 7.2.3 Priority Setting 7-12 7.2.3.1 Criteria for Ranking Priority Strategies 7-12 7.2.3.2 Determining Priority Strategies 7-12 7.2.3.3 Scheduling Priorities 7-12 7.3 Categories of Implementation 7-13 7.3.1 Strategies by Implementation Category 7-13 7.4 TOC Priorities for Year One [still in draft] 7-14 Part IV: References 8.0 Bibliography 8-1 8.1 Chapter 1 8-1 8.2 Chapter 2 8-2 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: Appendixes A. Acronyms A-1 B. Glossary B-1 C. Oversize Maps C-1 D. Comprehensive Species List of San Diego Bay D-1 D.1 References D-27 E. Species and Their Habitats E-1 E.1 References E-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-1 xi 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 Policy H-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 to Disturbance: A Basis of Policy Development H-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 Marsh—Subtidal 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, 1994–1997.* 2-80 2-13. Biomass of Fishes in San Diego Bay by Station, 1994–1997. 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, 1994–1997. 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. 6-25 xiii 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 1994–April 1997. 2-84 2-9. Total Number of Individuals and Biomass (g) of Fish Species Taken at the North-Central Bay (Station 2), July 1994–April 1997. 2-85 2-10. Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay (Station 3), July 1994–April 1997. 2-86 2-11. Total Number of Individuals and Biomass (g) of fish Species Taken at the South Bay (Station 4), July 1994–April 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. 3-29 xiv 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 Port’s Tidelands, 1999–2008, Pertinent to this INRMP. 3-37 3-9. Uniform Tourist Tax Collections, FYs 1988–1996, 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, 1993–1998.4-82 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 Bay’s 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-3 xv 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 1993–1994. 2-99 2-9. Biodiversity of Birds Based on Three Surveys Conducted in 1993–1994. 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 (1997–2002). 3-35 4-1. Past Mitigation Projects in San Diego Bay. 4-45 4-2. Protected Marine and Coastal Habitat in San Diego Bay—1998. 4-57 5-1. San Diego Bay Oil Spills Reported to US Coast Guard (1993–1996). 5-63 C-1. Habitats of San Diego Bay. C-3 C-2. Mean Numerical Density of All Fish Species January Samples, 1994–1997. C-5 C-3. Mean Numerical Density of All Fish Species July Samples, 1994–1997. C-7 C-4. Mean Biomass Density of All Fish Species January Samples, 1994–1997. C-9 C-5. Mean Biomass Density of All Fish Species July Samples, 1994–1997. 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. Belding’s 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. 5-26 xvii 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 Plan Reference: 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; Natural Resources 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 permission of the U.S. Department of the Navy, Southwest Division and San Diego Unified Port District ii September 2000
  • 21. San Diego Bay Integrated Natural Resources Management Plan San Diego Bay Integrated Natural Resources Management Plan This Plan was prepared during 1997–2000 under the direction and advice of the following: Technical Oversight Committee US Navy, Southwest Division Jerry R. Boggs, Ph.D., Chair US Navy, Commander Naval Region Southwest Margaret Lenz, Tamara Conkle 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 Game Bill Tippets California Department of Fish and Game Marilyn Fluharty Friends of South Bay Wildlife James Peugh National Marine Fisheries Service Robert Hoffman San Diego Association of Governments Michael McLaughlin The Environmental Trust Don Hunsaker, Ph.D. US Army Corps of Engineers David 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 Consultant Elizabeth Copper CSU Northridge Larry 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 US Navy, Southwest Division Jerry R. Boggs, Ph.D., Chair US Navy, Commander Naval Region Southwest Margaret Lenz US Navy, Southwest Division Gaston Bordenave US Navy, Southwest Division Kevin McKeag Naval Air Station North Island Jan Larson Naval Command Center Operations Specialist Don Lydy Naval Station 32nd Street Mary Ann Flanagan National Park Service, Cabrillo National Monument Carol Knipper US Coast Guard Maritime Safety Lt. M.T. Cunningham iii September 2000
  • 22. San Diego Bay Integrated Natural Resources Management Plan This plan was prepared by: Project Manager Planner-In-Charge Marine Biologist Research, GIS, and Layout and Design Wildlife Illustration Tierra Data Systems Sommarstrom and Assoc. Richard Ford, Ph.D. Editing Catherine Lush Peter Else Elizabeth M. Kellogg Sari Sommarstrom, Ph.D. Department of Biology Cynthia Booth 208 O’Keefe Street 403 South 8th Street 10110 W. Lilac Rd. P.O. Box 719 S.D.S.U. Danielle Booth Menlo Park, CA 94025 Laramie, WY 82070 Escondido, CA 92026 Etna, CA 96027 5500 Campanile Drive Sherman Jones (650) 327-9201 (307) 755-1837 (760) 749-2247 (530) 467-5783 San Diego, CA 92182 James L. Kellogg fax (650) 327-9224 fax (760) 751-9707 Nancy McDonald Peter McDonald Keri Salmon Scott 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 Plan Approving Officials: Commander, Naval Bases San Diego Date Chair, Board of Port Commissioners Date San Diego Unified Port District Field Supervisor Date Carlsbad Field Office U.S. Fish and Wildlife Service Regional Director Date Region V California Department of Fish and Game Regional Administrator Date National Marine Fisheries Service v 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 Summary Part I: Introduction Chapter 1.0 Welcome to the Plan 1-1 1.1 The Plan: Why, What, and Where 1-1 1.1.1 The Plan’s Goal 1-2 1.1.2 Plan Origin 1-2 1.1.3 Purpose 1-4 1.1.4 Planning Zones 1-5 1.1.5 Roles of Plan Collaborators 1-5 1.1.6 Missions of US Navy and Port 1-10 1.1.7 Relationship to Other Regional Plans 1-10 1.1.8 Relationship to Local Plans 1-11 1.2 San Diego Bay: An Important and Sensitive Resource 1-12 1.2.1 Values 1-12 1.2.2 Key Management Issues 1-13 1.3 Ecosystem Management Framework 1-14 1.3.1 Defining Ecosystem Management 1-14 1.4 Strategic Design of Plan 1-15 1.4.1 Audience 1-15 1.4.2 Intent of Use 1-16 1.4.3 Organization 1-16 1.4.4 Implementation 1-17 1.4.5 Updating 1-18 Part II: State of the Bay Chapter 2.0 State of the Bay—Ecosystem Resources 2-1 2.1 Ecoregional Setting 2-2 2.2 Physical Conditions 2-2 2.2.1 Climate and Hydrography 2-2 2.2.2 Sediment 2-4 2.2.3 Water 2-8 2.2.3.1 Turbidity 2-8 2.2.3.2 Circulation, Temperature, and Salinity 2-8 2.2.3.3 Residence Time of Water 2-9 2.2.3.4 Hydrodynamic Regions of the Bay 2-10 2.3 Water and Sediment Quality 2-10 2.3.1 Historical Conditions 2-10 2.3.2 Current Conditions 2-14 2.3.2.1 Contaminants 2-14 2.3.2.2 Coliform Contamination 2-17 2.3.2.3 Other Water Quality Conditions 2-17 vii September 2000
  • 26. San Diego Bay Integrated Natural Resources Management Plan 2.3.3 Regional Comparisons 2-18 2.3.4 Ecological Effects 2-18 2.4 Bay Habitats 2-20 2.4.1 Deep Subtidal 2-20 2.4.2 Moderately Deep Subtidal 2-25 2.4.3 Shallow Subtidal 2-26 2.4.3.1 Unvegetated Shallow Soft Bottom 2-26 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 Substrate 2-41 2.4.5 Salt Works 2-44 2.4.6 Upland Transitions 2-46 2.4.6.1 Beaches and Dunes 2-47 2.4.6.2 Coastal Created Lands and Disturbed Uplands 2-49 2.4.6.3 Freshwater Wetlands and Riparian 2-50 2.4.6.4 River Mouths 2-51 2.5 Species Assemblages 2-52 2.5.1 Plankton 2-52 2.5.1.1 Phytoplankton 2-53 2.5.1.2 Zooplankton 2-55 2.5.1.3 Ichthyoplankton 2-55 2.5.2 Algae 2-58 2.5.2.1 Macroalgae 2-58 2.5.3 Invertebrates 2-60 2.5.3.1 Invertebrates of Soft Bottom, Unconsolidated Sediment 2-61 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 Habitat Disturbance 2-67 2.5.4 Fishes 2-69 2.5.4.1 Description 2-69 2.5.4.2 Species Composition Baywide 2-72 2.5.4.3 Rankings Based on Ecological Index 2-72 2.5.4.4 Comparison of Total Abundance and Biomass Among Bay Regions 2-73 2.5.4.5 Comparisons of Species Abundance and Biomass by Region 2-73 2.5.4.6 Seasonal Changes in Abundance and Biomass 2-78 2.5.4.7 Patterns of Biodiversity and Species Assemblages in Four Regions of the Bay 2-79 2.5.4.8 Functional Groups of Fishes 2-83 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 Niño 2-89 2.5.4.11 Correlation of Fish Abundance With Environmental Factors 2-89 2.5.4.12 Possible Sensitive Habitats or Nursery Area for Fishes in San Diego Bay 2-90 2.5.5 Birds 2-90 2.5.6 Marine Mammals 2-104 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 Accounts 2-106 2.5.7 Exotic Marine and Coastal Species 2-108 2.5.7.1 History and Background 2-109 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 Species 2-117 2.6.1 Federally Listed Species 2-118 2.6.1.1 Green Sea Turtle 2-118 2.6.1.2 California least tern 2-121 2.6.1.3 Light footed clapper rail 2-124 2.6.1.4 California brown pelican 2-125 2.6.1.5 Western snowy plover 2-126 2.6.1.6 Sand dune tiger beetle 2-127 2.6.1.7 Salt marsh bird’s beak 2-127 2.6.2 State Listed Species and Species of Concern 2-128 2.7 The Ecosystem as a Functional Whole 2-129 2.7.1 Ecosystem Attributes 2-129 2.7.2 Physical Structure 2-131 2.7.3 Community Organization 2-131 2.7.3.1 Nutrient Cycling 2-133 2.7.3.2 Primary Production 2-133 2.7.3.3 Energy Transfer Through Food Webs 2-134 2.7.3.4 Biodiversity 2-136 2.7.4 Disturbance Regimes and Time Scales of Change 2-136 2.8 State of Ecosystem Health: Information Needs Assessment 2-137 2.8.1 What We Need to Know to Describe the State of the Bay Ecosystem 2-138 2.8.2 What We Currently Understand About Bay Ecosystem Health 2-139 Chapter 3.0 State of the Bay—Human Use 3-1 3.1 Ecological History of Human Use 3-3 3.1.1 Summary of Human Use and Change 3-3 3.2 The Bay Region’s Human Setting 3-6 3.2.1 Area and Population 3-6 3.2.2 Land Use and Ownership 3-7 3.2.2.1 Bay Water and Tidelands 3-7 3.3 Current Patterns of Use 3-9 3.3.1 Navy Plans and Uses 3-9 3.3.2 Port Plans and Uses 3-14 3.3.3 Local Plans 3-17 3.3.4 Recreation and Tourism Uses 3-17 3.3.5 Navigation 3-21 3.3.6 Fisheries 3-21 3.4 Future Patterns and Plans at the Bay 3-24 3.4.1 Navy 3-24 3.4.2 Port 3-26 3.4.3 City Plans 3-28 3.5 Economics of Use 3-28 3.5.1 Navy 3-28 3.5.2 Port 3-28 3.5.3 Fisheries 3-29 3.5.4 Recreation and Tourism 3-29 3.5.5 Other Uses 3-30 3.6 Overview of Government Regulation of Bay Activities 3-30 3.6.1 Introduction 3-30 3.6.2 Federal Agencies and Laws 3-32 3.6.3 State Agencies and Laws 3-34 3.6.4 Local Agencies and Laws 3-38 3.6.5 Project Mitigation Under NEPA and CEQA 3-39 ix September 2000
  • 28. San Diego Bay Integrated Natural Resources Management Plan Part III: Management Strategies Chapter 4.0 Ecosystem Management Strategies 4-1 4.1 San Diego Bay’s Natural Resource Values and Ecosystem Management 4-2 4.2 Habitat Protection and Management 4-2 4.2.1 Strategy by Habitat 4-2 4.2.1.1 Deep Subtidal 4-2 4.2.1.2 Moderately Deep Subtidal 4-6 4.2.1.3 Unvegetated Shallow Subtidal 4-7 4.2.1.4 Vegetated Shallow Subtidal 4-11 4.2.1.5 Intertidal Flats 4-14 4.2.1.6 Salt Marsh 4-19 4.2.1.7 Artificial Hard Substrate 4-24 4.2.1.8 Salt Works 4-30 4.2.1.9 Upland Transitions 4-33 4.2.1.10 River Mouths and Floodplains 4-36 4.2.2 Mitigation and Enhancement 4-37 4.2.3 Protected Sites 4-50 4.3 Species Population Protection and Management 4-61 4.3.1 Exotic Species 4-61 4.3.2 Plankton 4-72 4.3.2.1 Benthic Algae 4-73 4.3.2.2 Invertebrates 4-74 4.3.3 Fishes 4-76 4.3.3.1 Harvest Management 4-78 4.3.3.2 Artificial Propagation 4-84 4.3.4 Birds 4-88 4.3.5 Marine Mammals 4-95 4.3.6 Sensitive Species Special Protections 4-99 4.3.6.1 Green Sea Turtle 4-99 4.3.6.2 California Least Tern 4-104 4.3.6.3 Light-footed Clapper Rail 4-107 4.3.6.4 Western Snowy Plover 4-108 4.3.6.5 Salt Marsh Bird’s Beak 4-109 4.4 Ecosystem Approach 4-111 Chapter 5.0 Compatible Use Strategies 5-1 5.1 Within-Bay Project Strategies 5-2 5.1.1 Dredge and Fill Projects 5-2 5.1.2 Ship and Boat Maintenance and Operations 5-17 5.1.3 Shoreline Construction 5-26 5.1.4 Water Surface Use and Shoreline Disturbances 5-35 5.2 Watershed Management Strategies 5-43 5.2.1 The Watershed Management Approach 5-43 5.2.2 Storm water Management 5-46 5.2.3 Freshwater Inflow Management 5-55 5.3 Cleanup of Bay Use Impacts 5-58 5.3.1 Remediation of Contaminated Sediments 5-58 5.3.2 Oil Spill or Hazardous Substance Prevention and CleanUp 5-66 5.4 Cumulative Effects 5-69 5.5 Environmental Education 5-72 Chapter 6.0 Monitoring and Research 6-1 6.1 Concepts and Models for Monitoring and Research 6-2 6.1.1 Tenets for Design of a Monitoring and Research Program 6-2 6.1.2 Key Management Questions 6-3 6.2 Program Elements 6-4 x September 2000
  • 29. San Diego Bay Integrated Natural Resources Management Plan 6.2.1 Long-term Monitoring for the Bay’s Ecological Condition and Trend 6-5 6.2.2 Project Monitoring 6-17 6.2.3 Research to Support Management Needs 6-19 6.3 Data Integration, Access, and Reporting 6-24 Chapter 7.0 Implementation Strategies 7-1 7.1 Achieving Success 7-2 7.2 Components of Implementation 7-3 7.2.1 Institutional Resources 7-3 7.2.1.1 Existing Organizations 7-3 7.2.1.2 Potential New Institutions and Mechanisms 7-4 7.2.2 Funding Resources 7-6 7.2.2.1 Existing Sources 7-7 7.2.2.2 Potential New Sources 7-11 7.2.2.3 Volunteer Contributions 7-12 7.3 Proposed Organizational Structure 7-12 7.4 Priority Setting 7-15 7.4.1 Criteria for Ranking Priority Strategies and Projects 7-15 7.4.2 Scheduling Priorities 7-16 Part IV: References Chapter 8.0 Bibliography 8-1 8.1 Chapter 1 8-1 8.2 Chapter 2 8-2 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: Appendices A. Acronyms A-1 B. Glossary B-1 C. Oversize Maps C-1 D. Comprehensive Species List of San Diego Bay D-1 D.1 References D-27 E. Species and Their Habitats E-1 E.1 References E-29 F. Narratives on Sensitive Species Not Listed Under Federal or State Endangered Species Acts F-1 F.1 References F-10 G. Ecological History of San Diego Bay G-1 G.1 References G-8 H. Habitat Protection Policies: Preliminary Concepts H-1 H.1 Draft Policy for Protection of Intertidal Flats H-3 xi September 2000
  • 30. San Diego Bay Integrated Natural Resources Management Plan H.2 Draft Policy for Protection of Unvegetated Shallows H-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-23 I. Public Comments and Responses I-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 Marsh—Subtidal 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, 1994–1999. 2-74 2-13. Biomass of Fishes in San Diego Bay by Station, 1994–1999. 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 the Northern 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, 1994–1997. 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. 7-13 xiii 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 1994–April 1999. 2-75 2-9. Total Number of Individuals and Biomass (g) of Fish Species Taken in the North-Central Bay (Station 2), July 1994–April 1999. 2-76 2-10. Total Number of Individuals and Biomass (g) of Fish Species in the South-Central Bay (Station 3), July 1994–April 1999. 2-77 2-11. Total Number of Individuals and Biomass (g) of Fish Species Taken in the South Bay (Station 4), July 1994–April 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 of Central 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 Effects Caused, 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, Mission Bay, 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 water transferred 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 Port’s Tidelands, 1999–2008, Pertinent to this INRMP. 3-27 3-8. Uniform Tourist Tax Collections, FYs 1988–1996, 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 Checklist 4-51 4-5. Marine and Coastal Habitat Areas in San Diego Bay That are Designated for Some Level of Protection 4-53 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, 1993–1998.4-81 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 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. 5-29 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 Bay’s Condition and Trend 6-10 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 Bay Water with Ocean Water during Tidal Cycles. The Data are based on a Two-Dimensional Hydrodynamic Model (depth not considered), validated with Salinity and Temperature Correlations. Data and Graphics provided by Don Sutton and John Helly of the San Diego Supercomputer Center. Legend on Graph says “Hours 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 1993–1994. 2-95 2-9. Biodiversity of Birds Based on Three Surveys Conducted in 1993–1994. 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 (1997–2002). 3-25 4-1. Past Mitigation Projects in San Diego Bay. 4-45 4-2. Protected Marine and Coastal Habitat in San Diego Bay—1998. 4-56 5-1. San Diego Bay Oil Spills Reported to US Coast Guard (1993–1996). 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, 1995–1999. C-5 C-3. Mean Numerical Density of All Fish Species July Samples, 1994–1998. C-7 C-4. Mean Biomass Density of All Fish Species January Samples, 1995–1999. C-9 C-5. Mean Biomass Density of All Fish Species July Samples, 1994–1998. 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 Bay’s 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, Including Gracilaria 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. Belding’s 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. 5-26 xix 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, tuni- cates, brittle stars, mud shrimp, bay mussels, sea pansies, eelgrass, salt marsh bird’s 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 major managers 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 also supporting the ability of the Navy and Port to meet their missions and continue functioning within the Bay. The ecosystem approach reflected in the Plan looks at the interconnections among 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 of individual species or sites or projects. Ensure the long-term health, recovery The Bay Ecosystem Plan’s goal is to: and protection of San Diego Bay’s ecosystem in concert with the Bay’s economic, Naval, recreational, navigational, and fisheries needs.
  • 40. San Diego Bay Integrated Natural Resources Management Plan This Plan is intended to be an agent of change. To this „ Plan and coordinate projects and activities so that end, beginning in Chapter 1, the Plan’s vision for San they are compatible with natural resources (Chapter Diego 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 and existing 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 Plan’s goal „ Conduct research and long-term monitoring that supports decision-making (Chapter 6); and and vision. They flesh out a progression not towards the historical Bay, because that is gone forever, but towards „ Put in place a Stakeholders’ Committee and Focus one that is wilder, with softer shorelines, richer and Subcommittees for collaborative, ecosystem-based more abundant in native life. They also describe a Bay problem-solving in pursuit of the goal and objec- that, while used for thriving urban, commercial, and tives (Chapter 7). military needs, has an increasing proportion of uses that are passive. It is moving towards a place with more A cooperative effort of many people brought this Plan opportunities for public access, recreation, education together. Besides representatives from the Navy and and enjoyment of the myriad benefits of a healthy, SDUPD, regulatory and resource agencies formed the dynamic ecosystem. Finally, the Bay’s managers and lead “umbrella” group called the Technical Oversight stakeholders will make sounder decisions because of Committee (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. Task ment strategies were considered in institutional, social, forces, committees, partnerships, cooperative agree- and economic contexts to validate the Plan’s ecosystem ments, memoranda of understanding, monitoring approach. Another advisory committee was the Navy strategies, research projects, award programs, informa- Installation Oversight Committee (NIOC), composed of tion 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. University The 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- xxii September 2000
  • 41. San Diego Bay Integrated Natural Resources Management Plan ment by those interests not represented on any of the remains has been modified by structures for shore- committees was actively sought. Public workshops were line 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 helped this 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 value Water Quality Panel of developed shorelines and marine structures and (SDBIWQP or “Bay their functional contribution to the ecosystem. New Panel”) met for five shoreline stabilization structures should be mini- years to develop a mized, and existing structures should be enhanced Comprehensive Man- as habitat for fish and wildlife. When new armoring agement Plan for San or reconstruction of degraded armoring is demon- Diego Bay (SDBIWQP strably unavoidable, it should be designed to incor- 1998). Water quality porate maximum practical habitat value for native issues were the main species, giving priority to solutions that use materi- focus of this effort, but als of the type indigenous to the Bay. There should a range of natural be 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 Plan which currently vary greatly in their ability to sup- incorporates many of the recommendations of the Bay port 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 involves SDUPD, US Navy, regulators and resource agencies. Key Findings and Strategies The Plan should set goals for protecting and enhanc- ing natural shoreline functions, prevent new shore- Habitats and Populations line impacts, restore shoreline functions as The shallower habitats and the Bay’s 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 a meal. The Plan should provide techniques for add- 42% loss of shallow subtidal areas. In contrast, deep water ing habitat value to structures as they need to be habitat has doubled since the Bay’s first dredging in 1914. replaced, and identify means to provide economic Also, 74% of the shoreline is now armored with artificial incentive 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 enhanced should be adopted by the resource and regulatory light penetration. Appro- agencies because current protection is considered priate preplanning inadequate. A draft policy is in Appendix H. should be conducted to take advantage of oppor- † The Plan allows for no net loss of shallow subtidal tunities for filling mod- habitat in acreage or in existing biological functions erately-deep habitats to and values, and seeks long-term enhancement of eel- shallow or intertidal ele- grass habitat. Continued enforcement of mitigation vations. standards under the Southern California Eelgrass Mitigation Policy is necessary. † Salt marsh acreage should be expanded and † This Plan seeks a long-term net gain of area, func- enhanced, as should the tion, value and permanence of intertidal flats, and linkages between salt the physical conditions which support this habitat. marsh and other habitats. Intertidal habitat encompasses the area between Some priority sites for high and low tides. Losses in this zone have been the enhancement include the most severe of all Bay habitats, and most of what north end of D-Street, xxiii September 2000
  • 42. San Diego Bay Integrated Natural Resources Management Plan north side of Gunpowder Point, E-Street marsh on the mented. The ecological functioning of the Otay River south side of Gunpowder Point, J-Street Marsh, the 100-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 include Commission (CCC) permits for new construction, the transport of plankton into and out of the Bay for especially for sensitive habitats such as the salt coastal species (such as the larvae of many fishes and marsh. 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 number new 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 fish landscaping designs (“bayscaping”) and wildlife by shoring them up to shallower, more should be encouraged. Bayscaping uses a productive 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 along the Bay’s shoreline to enhance habitat value, prevent pollution, conserve water, and control exotic intro- ductions. A demonstration brochure should be dis- Populations tributed, and an award system should be promoted † This Plan places a high priority on the long-term that recognizes the best use of appropriate landscape protection and monitoring of both plant plankton designs. High priority enhancement sites in the and zooplankton. Zooplankton include the eggs and upland transition are vacant parcels along the south- larvae of fish and crustaceans that need to drift into west shore such as: Emory Reserve, South Bay shallow or intertidal Bay waters from the open ocean Marine Biological Study Area, and the parcel leased to complete their juvenile life stages. by the US Navy to California Department of Parks and 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 be add structure to the habitat and should analyzed 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 salt tecting the substrate and water quality extraction 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 for It represents one of the few large feeding, roosting, and human consumption through studies that assess the nesting areas remaining along the urbanized southern effects of toxics and their severity. California coast. Enhancement should be targeted for † San Diego Bay’s 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 mouths enhancement. The warm water temperatures and as natural corridors and buffers between salt water high productivity during the spring and summer and freshwater habitats should be examined and months in shallow and intertidal waters enable the enhanced to more nearly approach their natural role. Bay to support large numbers of larval and juvenile Today, streams draining into the Bay are channelized fishes. 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, and episodic siltation function formerly played by thus contribute to the biodiversity of fish populations. uncontrolled streams should be identified and imple- † This Plan targets an increase in the Bay’s carrying capacity for shorebirds, nesting seabirds, and marsh and upland transition resident birds. It advocates establishing specific population targets for priority xxiv September 2000
  • 43. San Diego Bay Integrated Natural Resources Management Plan bird 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 numbers tory birds on the Pacific Flyway. More than 305 bird of 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, are Other management activities for the protection of migratory and rely on the Bay as an important rest- sensitive species are habitat-based, as described above. ing and feeding stopover. Others, especially those arriving from tropical latitudes, spend the winter, Compatible Use of the Bay’s Natural Resources breed or nest. One-third of birds dependent on San Diego Bay have been identified as sensitive or declin- Mitigation and Enhancement ing by the federal or state governments or by the An improvement is sought in the effectiveness and success Audubon Society. of mitigation and enhancement projects by building a † Secure nesting sites for colonial seabirds should be consensus of prioritized need among regulators and provided that allow for project proponents. population recovery by managing predators and enhancing habitat. Coop- erative agreements on predator management that result in more effective protection 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 functions ation 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 the species are found in the Bay’s planning zone. Bay should be maximized, consistent with the habitat Ballast water controls are necessary. The USCG objectives 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 as cial reuse site for habitat restoration or enhancement necessary. The Navy’s ballast water exchange policy in the Bay should be identified so that project sponsors for open-ocean exchange should continue, and the from multiple jurisdictions may contribute jointly to implementation of a ballast water management pro- an enhancement project over time and as dredge mate- gram that explicitly addresses the nonindigenous rial accumulates. invasive species problem is encouraged. Dredging The number of new invasive exotic species should be When dredging is necessary it should be conducted in an reduced or prevented by educational and preventive environmentally sound manner. methods. For example, appropriate landscaping and restoration practices that control the introduction of † Ecosystem processes, habitat values and species that invasive exotic plants are encouraged. are affected by dredging should be documented and described in sufficient detail to ensure adequate mit- The City of San Diego should designate the Bay as igation. For example, at intertidal sites the habitat “open space” for the purposes of its Biological Mitiga- functions and values for fishes, invertebrates and tion Ordinance, prohibiting the use of invasive exotic shorebirds should be detailed so that all are plants 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 minimized formed which is composed of resource managers, close to shore, in order not to contribute to further researchers and interested public to implement the loss of intertidal habitats and the need to armor the above strategy. The Task Force should oversee an shoreline. Prioritize new dredging at locations where Exotic 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 a Many other sensitive species occur in and around means to combine habitat enhancement with near- shore confined disposal sites. xxv September 2000
  • 44. San Diego Bay Integrated Natural Resources Management Plan Recreational Harvesting habitat 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. † SDUPD’s Boater’s 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) increase be minimized by establishing setbacks for new con- censusing of California halibut and sand bass; struction and other strategies near important nesting 3) 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 catches back requirements near marshes. can be considered separately from those in the ocean; Ecotourism and 4) encourage a bait fishery monitoring program, † The potential for ecotourism development related to such as for ghost shrimp. To accomplish this, stable birdwatching should be pursued, and use of public revenue sources to supplement license revenues for lands for this purpose encouraged in a manner con- the California Department of Fish and Game’s sistent with maintaining local resource values. (CDFG) enforcement efforts are sought. Water and Sediment Quality Management Ship 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 Committee green vegetated buffers at marina sites where possi- should be a core group of the Task Force. The Task ble to filter runoff into the Bay, and 2) moving power Force should develop watershed problem and need wash 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 that and 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 with through 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 coating’s effectiveness in terms of durability, bonding and repel- Cumulative Effects lency of fouling organisms under local conditions. The format by which cumulative effects are discussed in Surface Water Use environmental 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 be properly 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 infor- mation clearinghouse on local extirpations or † The Plan advocates seasonal restrictions for water- declines of species at risk. Project areas should be craft in priority bird-use areas. Practical steps, such as properly identified and bounded such that all other watercraft speed reduction, noise and light reduction projects that overlap in time and space with a project or shielding, and avoidance of bird assemblages and area boundary are considered. The target manage- ment species identified in this Plan should be used to help focus the analysis of potential impacts. xxvi September 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 the long-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 among nonprofit organizations, government, schools, and † Target management species should be selected for long-term or periodic monitoring to provide a focus businesses 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 particular walks 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 success ibut, 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 the ment monitoring, continuance of environmental education programs including a citizen- about San Diego Bay. Explore use of a “bed-tax” from based program to visitors’ 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 estab- lished to make deci- 1. Planning, management, monitoring, and research sions on long-term are 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 effective The 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 management watershed, 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 support lated 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 proposed posed to act as management cues represent both that involves a Priority Problem List and the ranking parts 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 Monitoring oritize research needs. The purpose of the Research A long-term monitoring program is a key element of the Committee will be to set research priorities in rela- Bay Ecosystem Plan’s strategies for better Bay manage- tion to management concerns, decide what manage- ment. 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 a tified for long-term monitoring. They are intended broad audience. to provide cues for adaptively managing the Bay’s natural resources. These include monitoring a core † Project-related research and monitoring can set of elements, such as the physical and chemical enhance learning and experience, such as to better characteristics of the water column and sediment, define the area affected by a project and cumulative chlorophyll, habitat quantity or quality change, effects, the strength of dependencies among habitats changes 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 as as 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 be Planning and Coordinating Projects used to encourage reliable comparisons among and Activities projects, 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 alternative mary purposes--to be an effective tool for project planners shoreline and underwater habitat structures that are and Bay managers. more beneficial to the environment should be facili- tated. If shown to be environmentally safe, durable, Tools for Accomplishing the Plan’s Goal strong and cost-effective, a replacement program for and Objectives all chemically-treated wood pilings with plastics It is the desire of everyone who worked long and hard on within the Bay should be promoted. A high priority this 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 Sharing off 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 Bay’s natural resources that is accessible to a broad range of users, both technical and nontechnical. The criteria for selection 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 range of involved parties, including a newsletter to report on progress in implementing this Plan and other Bay activities, biannual reporting on the “State of San Diego Bay,” workshops and conferences, and cross- disciplinary field programs. xxviii September 2000
  • 47. San Diego Bay Integrated Natural Resources Management Plan Part I: Introduction
  • 48. San Diego Bay Integrated Natural Resources Management Plan 1.0 Welcome to the Plan “This Port of San Diego is beautiful to behold, and does not belie its reputation.” Father Serra, 1769 1.1 The Plan: Why, What, and Where Marinas, 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 bird’s 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-term strategy for two of the major managers of the Bay: the US Navy and the San Diego Unified 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 and the Port to meet their missions and continue functioning within the Bay. September 2000
  • 49. San Diego Bay Integrated Natural Resources Management Plan A new approach reflected in the Plan is to look at the interconnections among all of 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 processes rather than as a collection of individual species or sites or projects. As such, this Plan was nicknamed the “Bay Ecosystem Plan.” This Plan is intended to be an agent of change. To this end, many new strategies and tactics for Bay managers are proposed. These include new, or changes in existing, policies for: † protecting Bay habitats and ecological processes; † planning for current and future uses, including for mitigation and enhancement, and analyzing for cumulative effects; and † developing a research and long-term monitoring program to support deci- sion-making. 1.1.1 The Plan’s Goal A Goal Statement is an essential component of a successful plan. “Goal” is defined here as “a broad statement of intent, direction and purpose; an enduring, visionary description of where you want to go.” A goal is not necessarily completely obtainable. However, its vision is used as the compass of a plan’s progress: are we continuing to move in the agreed upon direction? Without the compass, a plan can easily wan- der off course. Goal—Ensure the long-term health, recovery, and protection of San Diego Bay’s ecosystem in concert with the Bay’s economic, Naval, recreational, navigational, and fisheries needs. Habitat conservation and restoration are implied in the first part of the Goal Statement, as well as protection of ecosystem processes that depend on these habitats, such as productivity, nutrient cycling, and support of a complex food web. These habitats and related processes are specifically addressed in objectives and strategies in later chapters. 1.1.2 Plan Origin Beginning in 1992, biologists within the Navy’s Southwest Division office, as well as from the US Fish and Wildlife Service (USFWS) and the National Marine Fisher- ies Service (NMFS), observed that project-by-project management of natural resources in San Diego Bay resulted in lengthy and often redundant efforts by the Navy and the regulatory agencies. Biologically, managing resources was frustrat- ing when based on political boundaries instead of natural, ecosystem boundaries. The project-by-project approach led resources to be managed on a very site-spe- cific basis. In 1993, these biologists began the collection of data necessary to the development of a Baywide resources management plan. „ Navy and agency biologists were In 1996, the Navy decided to prepare an Integrated Natural Resource Manage- frustrated with project-by-project ment Plan (INRMP) for San Diego Bay that would address Navy-owned and -con- management of the Bay within trolled tidelands and waters only. Already, INRMPs had been completed for the political, instead of natural, boundaries. land portion of each Naval installation around the Bay, as required by Navy pol- icy (Chief of Naval Operations Instruction [OPNAVINST] 5090.1B), but not for the water or Bay as a whole. The Navy had decided that a “big picture” approach to managing the Bay’s resources and planning for future needs would prove more valuable in the long run than a piecemeal approach. 1-2 Welcome to the Plan September 2000
  • 50. San Diego Bay Integrated Natural Resources Management Plan Photo 1-1. Aerial Photo of San Diego Bay Region. Welcome to the Plan 1-3 September 2000
  • 51. San Diego Bay Integrated Natural Resources Management Plan „ The Port also wanted to avoid Sharing similar experiences, the SDUPD became interested in working collaboratively piecemeal management and with its neighbor on a single natural resource plan for the Bay. As a result, the Board of signed on as a partner with its Port Commissioners voted on January 7, 1997 to become a partner with the Navy in Navy neighbor in January 1997. jointly developing a natural resource management plan for the Bay, expressing con- cern that “a balance be achieved in designating sites for mitigation and preserving the valuable natural resources while not precluding development opportunities.” This Plan builds on an earlier planning effort by the Port, the South San Diego Bay Enhancement Plan (Macdonald et al. 1990). Environmental community interests and pressures also contributed to the widely felt need for a Baywide plan. Representation from the nongovernment environmental community in the planning process was sought in response to this interest. Contributing to the Plan’s information base are surveys of natural resources funded by the Navy between 1993 and 1997, with contributions from the Port and other agencies. 1.1.3 Purpose This INRMP provides the goal, objectives, and policy recommendations to guide planning, management, conservation, restoration, and enhancement of the San Diego Bay ecosystem. It also provides support to the US Navy and the Port mis- sions. As such, it will serve as a nonregulatory guide to better, more cost-effective decisions by those involved with the Bay. „ This Plan serves as a nonregula- The Plan meets some particular needs of the principal proponents, the US Navy tory guide to improved, more and the Port of San Diego, as well as the regulatory community: cost-effective decisions by the Navy, Port, and other decision- 1. Improved coordination by the Navy and Port and other natural resource makers for the Bay’s resources. managers for managing, protecting, and restoring the Bay’s ecosystem. 2. Recognition of the current status of the Bay’s natural ecosystem, and mak- ing the information that supports this status broadly available. 3. Recognition of the current status of human use of the Bay’s ecosystem. 4. Development of practical management strategies for the Bay’s ecosystem to reach conservation, restoration, and enhancement objectives. 5. More effective support for project planning and compatible use of the Bay. 6. Identification of long-term ecosystem monitoring and research priorities needed to make better management decisions. 7. Timely and effective implementation of the recommended strategies, includ- ing an annual meeting to serve as a forum to discuss proposed projects, man- agement priorities, and mitigation and enhancement strategies. These seven purposes are parallel to and are reflected in the titles and contents of Chapters 1 through 7 of the Plan. „ No special emphasis is given to Certain topics, particularly water quality, as it relates to contaminant regulation, or water quality or endangered spe- endangered species and take permits, are not considered in depth because of their cies issues. These are well-covered coverage in other plans or processes. The Plan instead addresses water and endan- in other plans and processes. gered species along with other important components. of the Bay ecosystem. By considering the Bay as one ecosystem that encompasses many political jurisdic- tions, the Plan covers the natural components as well as the geographic and time scales necessary to address the ecosystem’s needs. 1-4 Welcome to the Plan September 2000
  • 52. San Diego Bay Integrated Natural Resources Management Plan 1.1.4 Planning Zones San Diego Bay is part of the greater ecosystem of the southern California Bight (SCB) (see Map 1-1 and discussion of the Bight in Section 2.1 “Ecoregional Set- ting”) and covers 10,532 acres (4,262 hectares [ha]) of water and 4,419 acres (1,788 ha) of tidelands around the Bay, according to Port maps (San Diego Uni- fied Port District 1995b). “Tidelands” legally include land below the historic (1850) mean high tide line; some are now filled in and developed (e.g. Lindbergh Field, Coronado golf course, Naval Amphibious Base). These developed fill areas are not intended to be a primary focus of the Plan, so they are not included in the Plan’s Functional Planning Zone, or “footprint.” „ Map 1-2 depicts the Plan’s “foot- The footprint was specially delineated for this Plan to reflect the current condi- print” or Functional Planning tions. As shown in Map 1-2, this zone includes everything bayward of the cur- Zone, an area amounting to rent mean high tide line west to Ballast Point, with the addition of the Salt Works 12,132 acres (4,912 ha). at South Bay and the entire Sweetwater Marsh National Wildlife Refuge (SMNWR) on the east. This area of water, tidelands, and land encompasses 12,132 acres (4,912 ha). Map 1-3 shows the Conceptual Watershed Influence Zone, an area of 277,129 acre (112,198 ha) directly linked to the Bay’s resources. This zone includes the Sweetwater River and Otay River drainages, small urban creeks (e.g. Chollas Creek) and stormwater drains flowing directly into the Bay, and portions of Sil- ver Strand and Point Loma. This zone includes the waterfront areas of the cities, Navy, and Port adjacent to the Bay. Watersheds are important to include in con- cept because of the functional connectivity and interrelationships between the Bay and upstream processes—biological, physical, and chemical. However, upper watershed issues affecting the Bay will take more time to address thor- oughly than can be done within the original time frame of this Plan. 1.1.5 Roles of Plan A cooperative effort of many people has brought this Plan together. As depicted in Collaborators Figure 1-1, each oval represents a category of Plan collaborators. Names and affilia- tions of the members within each group can be found on the credit page of this Plan. „ Figure 1-1 shows the various The primary “umbrella” group is the Technical Oversight Committee (TOC). groups and processes involved in This diverse group of thirteen different organizations, represented by eighteen collaborating on the Plan. Deci- individuals, was created to include those entities that are most directly affected sion-making was centered in the Technical Oversight Committee, by the Plan and could contribute significantly to its development. The size of the representing thirteen diverse TOC was purposely limited since it had the role of making cooperative, consen- groups. Consensus was sought on sus-based decisions about the Plan’s approach, content, policy, and implementa- all parts of the Plan. tion. The members also provided professional and personal experience, scientific data, and a “reality check” on the material and ideas used. Their vary- ing perspectives helped ensure that ecosystem management strategies were con- sidered in institutional, social, and economic contexts to validate the Plan’s ecosystem approach. Meeting bimonthly or monthly since November 1996, the TOC has used its meetings as a forum for sharing information, debating key issues, and making decisions. Drafts of the Plan were first reviewed, discussed, and approved by the TOC on a consensus basis. Another advisory committee is the Navy Installation Oversight Committee (NIOC), composed of representatives from each of the major Navy installations around the Bay as well as from the US Coast Guard (USCG) and Cabrillo National Monument. This committee met as needed and provided data, profes- sional experience, and a check on the Plan’s consistency with the Navy mission. Welcome to the Plan 1-5 September 2000
  • 53. San Diego Bay Integrated Natural Resources Management Plan Map 1-1. San Diego Bay, the “Conceptual Watershed Influence Zone,” in the Southern California Bight. 1-6 Welcome to the Plan September 2000
  • 54. San Diego Bay Integrated Natural Resources Management Plan Map 1-2. San Diego Bay INRMP Functional Planning Zone, or “Footprint.” Welcome to the Plan 1-7 September 2000
  • 55. San Diego Bay Integrated Natural Resources Management Plan Map 1-3. San Diego Bay INRMP Functional Planning Zone and Conceptual Watershed Influence Zone. 1-8 Welcome to the Plan September 2000
  • 56. San Diego Bay Integrated Natural Resources Management Plan Other Interests Public/Private Workshops Bay Resource Technical Oversight Stakeholders Committee Navy Tenants SDUPD Tenants Navy Installation Workshops Oversight Committee Science Advisory Plan Facilitators Consultants and Advisors & Review Team INRMP Ecosystem Management Framework for San Diego Bay Figure 1-1. Roles of Plan Collaborators. Public comment by those interests not represented on any of the committees was actively sought. Public workshops sponsored by the TOC in July 1997, July 1998, and September 1999 were advertised widely, including several television interviews. Each workshop was attended by 20 to 50 people. Verbal and written comments helped identify new data sources, important issues for the Plan, and some recom- mendations on strategy. University and consultant scientists were asked to participate on the Science Advisory and Review Team, based on their area of expertise and willingness to serve. Diverse specialties were represented. Their role was to provide and help frame the Plan from an ecosystem perspective, to bring scientific data as well as imagination and creativity to the problem, and to share professional knowledge about the functioning and history of the Bay ecosystem. Serving in the role as staff was the Consultant, Tierra Data Systems, and their subcontractors. The consultant was to assemble the available scientific informa- tion into an ecosystem management framework for consideration by the TOC, assemble the needed technical people, facilitate better decisions by stimulating the imagination and creativity of the group, and integrate the complexities and uncertainties of all of the above into potential strategies. Welcome to the Plan 1-9 September 2000
  • 57. San Diego Bay Integrated Natural Resources Management Plan 1.1.6 Missions of US Navy US Navy and Port It is the mission of the US Navy in San Diego Bay and its environs to equip, main- tain, train and support Naval surface and aviation units of the Pacific Fleet in order to conduct military operations in support of the Fleet’s operational com- manders. Additionally, the US Navy in San Diego Bay will conduct Naval opera- tions in the eastern and northern Pacific Ocean, protecting the western sea approaches to the United States. The Bay’s Naval installations are described in detail in Chapter 3 “State of the Bay—Human Use.” San Diego Bay is said to be home to the largest Naval com- plex in the free world, leading one Navy captain to observe, “To say that it is impressive, spectacular, even dazzling to the uninitiated and uninformed is an under- statement on the order of saying Pavarotti can sing a little” (Halpern 1991). Beyond the Navy’s immediate mission at San Diego Bay is the US Department of Defense’s (USDoD) mission to prevent pollution, protect the environment, and protect natural, historic, and cultural resources (US Department of the Navy 1994; US Department of Defense 1996). Stewardship responsibilities for natural resources on all USDoD installations are emphasized in its regulations. USDoD’s Ecosystem Initiative (1996) states that “ecosystem management is a process that considers the environment as a complex system functioning as a whole, not as a collection of parts, and recognizes that people and their communities are part of the whole.” San Diego Unified Port District Created in 1962 by an act of the state legislature and approved by area voters, the SDUPD is a special-purpose unit of government. It was established to manage the harbor, operate the international airport at Lindbergh Field, and administer the public tidelands “in order to further the development of commerce, naviga- tion, fisheries and recreation” (San Diego Unified Port District 1995a). Displayed prominently at the SDUPD office is this Vision Statement: “Visionary people in partnership, propelling economic growth while creating the most excit- ing, dynamic and environmentally sensitive place to live, work and play. Come aboard!” Its recent Mission Statement is “A public benefit corporation providing avi- ation, maritime, and real estate services and infrastructure to enhance the regional economy, while providing recreational opportunities and protecting the tideland trust resources.” The Chairman of the Board of Port Commissioners remarked in 1998 that “As the Port strives to increase maritime trade and plan further waterfront development for the public good, we must continue our careful stewardship of the San Diego Bay ecosystem” (Malcolm 1998). 1.1.7 Relationship to Several related, regional efforts have gone on concurrently with this Plan. The San Other Regional Plans Diego Bay Interagency Water Quality Panel met for five years to develop a Com- prehensive Management Plan for San Diego Bay (San Diego Bay Interagency Water Quality Panel 1998). Water quality issues were the main focus of this effort, but also addressed were a range of natural resource, wildlife, and human use issues. The panel offered recommendations to the California Regional Water Quality Control Board (RWQCB) and other agencies active on the Bay. Pertinent data gathered during the effort were stored at the San Diego Supercomputer website. On related issues, this INRMP reiterates and can carry on the work of the Bay Panel, as well as help implement some of its recommendations. However, the intent is not to overlap with water quality regulatory issues. 1-10 Welcome to the Plan September 2000
  • 58. San Diego Bay Integrated Natural Resources Management Plan „ Water quality and endangered The southwestern region of San Diego County is covered by the City of San Diego’s species are the focus of at least Multiple Species Conservation Plan (MSCP). The cities of San Diego and Chula two other Plans. The Bay Ecosys- Vista, among others, are active participants in the MSCP and have jurisdiction over tem Plan will complement these efforts where applicable. some Bay marsh lands and waters. This regional habitat conservation plan is aimed at protecting multiple species and their habitats in place of the single species protec- tion approaches of the past (San Diego Association of Governments 1995; City of San Diego and MSCP Policy Committee. 1996). By creating an interconnected habi- tat preserve system for the region, and obtaining approval from the regulatory agen- cies, the local governments and landowners can receive permission to “take” species listed under the state and federal endangered species acts. Their plan is complete and was recently adopted by both the City and County of San Diego (City of San Diego and US Fish and Wildlife Service 1997). Funding for implementation is the next step. With the MSCP’s emphasis on terrestrial habitats, little overlap occurs between the two planning efforts. The only part of the Bay conserved by the MSCP is the privately owned sections in and adjacent to the Western Salt Company ponds in the southeast corner (US Fish and Wildlife Service 1998). „ Useful databases and a listing of In 1990, a South San Diego Bay Enhancement Plan was prepared for the Port and enhancement options were pro- the California State Coastal Conservancy (Macdonald et al. 1990). One of its pur- vided by the Port’s 1990 South San poses was to provide a comprehensive ecological baseline and historical perspec- Diego Bay Enhancement Plan. tive that could be used as guidance for environmental projects to maintain, enhance, restore, mitigate, or create natural resource values. The South Bay Plan was never adopted by the boards of either agency and the plan was deemed “infor- mational” rather than “advisory.” Its scope was south of the Sweetwater Channel only, and focused on identifying enhancement and mitigation opportunities for tidelands and submerged lands within the Port’s jurisdiction that were not desig- nated for development in the Port’s master plan. While narrower in scope than this INRMP, the 1990 South Bay Plan provides a useful synthesis of historic data, includes additional field survey data (particularly for birds), and identifies some alternative strategies for enhancement. This area is now encompassed in the newly-dedicated South San Diego Bay Unit of the San Diego National Wildlife Ref- uge (US Fish and Wildlife Service 1998), as well as the Bay Ecosystem Plan. San Diego Association of Governments (SANDAG) has recently prepared a Water Quality Element to its Regional Growth Management Strategy (San Diego Associa- tion of Governments 1997c). Its purpose is to address measures that can be incor- porated into development planning and environmental review processes to improve the region’s water quality and protect surface and groundwaters. As a source of recommended actions, this document is reflected in relevant water qual- ity strategies in the Bay Ecosystem Plan. 1.1.8 Relationship to Local land use planning is performed by each incorporated city and the county. Local Plans The cities of Chula Vista, Coronado, Imperial Beach, National City, and San Diego as well as San Diego County have all adopted general plans and implemented zon- ing ordinances, as required by the state. Within general plans are elements (e.g. Land Use, Conservation, Open Space) that may or may not address San Diego Bay’s natural resources. Sensitive resources such as wetlands, wildlife corridors, and threatened habitats can be designated, with adoption and implementation of resource protection ordinances (as cited in San Diego Association of Governments 1992). Since the Port and the state have jurisdiction on most of the Bay’s nonfed- eral tidelands and submerged lands, the city and county plans can only recom- Welcome to the Plan 1-11 September 2000
  • 59. San Diego Bay Integrated Natural Resources Management Plan mend changes in use within these areas, while applicants must apply to the Port and state for leases or change in leases. The local general plans and the Port master plan overlap in these sites. In addition, the California Coastal Act (CCA) requires each local government with property within the coastal zone to prepare and adopt a Local Coastal Plan (LCP), which has more stringent environmental protections than a general plan. Once certi- fied by the California Coastal Commission (CCC), a LCP is used as the basis for local government approval of proposed developments. Each local entity in the San Diego Bay region has an adopted and certified LCP, with amendments sent periodically to the CCC for approval. The Port’s Master Plan is considered their LCP. The intent of this INRMP is to exchange information and strategies with local planning efforts. 1.2 San Diego Bay: An Important and Sensitive Resource 1.2.1 Values Framed by palm trees, boats, or the Coronado Bridge, San Diego Bay provides a scenic backdrop for many picture postcards. Its presence is almost synonymous with the region. With its sheltered harbor, the Bay naturally attracted the US Navy to base a large portion of its Pacific Fleet in San Diego. Today more than 25% of the American Naval fleet is homeported here, amounting to 75 ships (including eleven submarines and two aircraft carriers). Over 87,000 sailors and 240,000 fam- ily members live and work in the San Diego area, with 29,000 civilian employees working at the Navy and Marine Corps bases. The USDoD’s annual financial ben- efit to San Diego’s economy is estimated at $10.6 billion (San Diego Bay Inter- agency Water Quality Panel 1998). Bay view From Point Loma. „ Together, the Navy and the Port The Port of San Diego refers to the Bay as “one of the most beautiful natural deep of San Diego generate an annual harbors in the world” and its coastal property as “among the most beautiful in the economic benefit of about world.” It is also proud of their achievements in creating jobs, providing public $18 billion to San Diego. access to the waterfront, and developing recreational opportunities along the Bay. Bayfront locations for real estate development and Port trade generate $7.4 billion annually in total economic impact (San Diego Unified Port District 1997). Yet the Bay’s function as a natural ecosystem is still largely a mystery. There are no postcards of the Bay’s underwater life, even though fascinating creatures like octo- pus, sea horses, butterfly rays, fiddler crabs, sand dollars, sea hares, and green sea tur- tles can be found here. Habitat and Species Richness Values of San Diego Bay (See also Appendix D). „ 280 species of dependent marine and coastal birds. „ 102 species of marine fish and one marine reptile. „ 621 species of marine invertebrates. „ 109 species of marine algae and plants. „ 9 species listed federal or state threatened or endangered. „ 823 acres (333 ha) of salt marsh. „ 978 acres (396 ha) of tidal flats. „ 1,065 acres (431 ha) of eelgrass beds. „ 45.4 miles (73.1 km) of hard substrate and fouling communities. „ 9,331 acres (3,776 ha) of mud and sand bottom assemblages in shallow to deep water. 1-12 Welcome to the Plan September 2000
  • 60. San Diego Bay Integrated Natural Resources Management Plan Underneath the water’s surface are aquatic communities that are only beginning to be understood by the scientific community, much less by the urban neighbors above. Historically, the Bay’s natural resources were valued only for their potential human use: whales and waterfowl for hunting, fish and shellfish for sport or com- mercial harvesting, wetlands for landfill sites. When garbage and pollution con- taminated the Bay during the first part of this century, the diversity of fish and wildlife was greatly reduced (Browning et al. 1973; Smith and Graham 1976). Earlier pollution stresses to the Bay have been reduced, but new pressures are challenging its ecological integrity and biodiversity. The control of waste dis- charges to the Bay in the 1960s initiated the recovery of the Bay’s ecosystem as well as its water quality (San Diego Unified Port District 1995b). Monitoring efforts largely focused on water quality measurements or on certain organisms (e.g. mussels, benthic invertebrates) as indicators of contamination. With the recognition in the 1970s and 1980s of the toxic effects of heavy metals and other contaminants in the sediments and waters of San Diego Bay, the health of the biological community was called into question. In the 1990s, human health advisories were issued for the consumption of the Bay’s fish and for water con- tact following rain storms because of coliform-contaminated runoff. However, human health advisories do not necessarily reflect ecological damage or risks. Concerns have been raised about the future security of the Bay’s remaining habi- tats and their dependent bird populations as pressures increase for more intensive use of the Bay’s shoreline and open water. With an increasing number of nonna- tive aquatic nuisance species also being found, the Bay’s ecological integrity is being challenged in many ways (Crooks 1997). Many agencies and organizations are working to protect the Bay’s resources, but a concerted approach has been lack- ing for its ecosystem. 1.2.2 Key Management To help provide focus to the planning process, an initial effort by the Plan’s TOC was Issues to list and discuss over 30 issues, some of which were suggested by the public at a July 1997 workshop. This list was revised and reworded to contain the following five key management issues: 1. Ensuring compatibility of Bay use with protection of natural resources. 2. Providing an ecosystem basis for planning, restoration, and management, including management of cumulative effects. 3. Building a shared information base that guides restoration and manage- ment of the Bay’s natural resources. 4. Limiting activities that negatively impact the health of the Bay. 5. Providing a strategy for successful implementation of the Plan across juris- dictions, including an organizational mechanism to pool resources and jointly oversee implementation. In addition to the above key issues, numerous specific concerns are listed and addressed in later chapters. Welcome to the Plan 1-13 September 2000
  • 61. San Diego Bay Integrated Natural Resources Management Plan 1.3 Ecosystem Management Framework Photo © 1999 San Diego Unified Port District Photo 1-2. San Diego Bay’s Urban Shoreline. 1.3.1 Defining Ecosystem The popularity of the words “ecosystem” and “ecosystem management” has Management caused some debate and confusion in their definition and use. To help with the intent of these terms as used in the Plan’s Goal Statement, definitions were agreed upon by the TOC. “Ecosystem” is commonly defined as “a unit of land or water comprising populations of organisms considered together with their physical environment and the interacting pro- cesses between them.” A natural resource dictionary offers this clarification: “While many definitions tend to emphasize the component parts present, it is the pro- cesses acting on and/or initiated by the component parts that make the ecosystem function. Without the vital processes, the system is dysfunctional or, worse still, nonfunctional” (Dunster and Dunster 1996). “Ecosystem management” is defined for the purposes of this Plan as “a manage- ment practice and philosophy aimed at protecting, maintaining, or enhancing the eco- system while providing resources, products, or nonconsumptive values for humans. It complements the time and space scales of environmental change and ecosystem response. Ecosystem management is realized through effective, collaborative partner- ships among government and nongovernment interests.” „ A separate, but compatible, defi- This definition is compatible with USDoD’s Ecosystem Initiative (see Section 1.1.6 nition comes from the USDoD. “Missions of US Navy and Port”). The above definition was derived from the USDoD definition as well as language suggested in two other sources (Dunster and Dunster 1996; Keystone Center 1996). 1-14 Welcome to the Plan September 2000
  • 62. San Diego Bay Integrated Natural Resources Management Plan The Ecosystem Management Approach What Ecosystem Management Means to the Bay Ecosystem Plan 1 Defining the Problem - Emphasis is placed on healthy ecological processes and linkages, and on whole habitats and communities rather than individual species or projects. - Problems are defined without regard to jurisdictional boundaries or technical disciplines, and cooperative solutions are sought when the problem crosses jurisdictional boundaries. 2 Assessing the State of the Bay—Natural and Human Components - Assessment and monitoring strategies are prioritized in part based on their ability to provide insight into the strength and dependencies of one habitat or community upon another, and into both the structure and functional processes of the ecosystem. - Assessment and monitoring strategies are prioritized in part based on their ability to detect long-term trends and the cause of significant ecosystem change. - Assessment and monitoring strategies are identified that shed light on how the Bay sustains vibrant, healthy, and economically diverse human activities. 3 Ecosystem Planning Process - Ecological, social, and economic goals are integrated. - The process involves diverse government and nongovernment groups coming together with significant participation by community stakeholders. 4 Management Strategies - Management works at multiple scales appropriate to the problem. - Market- and incentive-based approaches are considered, as well as the need for regulation. - Management approaches, including projects and mitigation, acknowledge the role of regula- tion in contributing to ecological and socio-economic objectives. 5 Implementation - Management and research are implemented at multiple scales appropriate to the understanding of the problem, and to encourage experimentation and innovation. Small-scale prototypes with adaptive management and maximum dissemination of learned information are advocated. - Emphasis is on cooperative, interjurisdictional, cross-boundary conservation partnerships, with potential new roles for government and nongovernment groups. - Project evaluation draws on socio-economic and political experience and expertise, as well as that of biologists and natural resource managers. 1.4 Strategic Design of Plan 1.4.1 Audience While developed primarily to facilitate the Navy and Port missions, this INRMP was prepared with many different users in mind: † The US Navy and the Port of San Diego, as the primary sponsors of this Plan. Included within the Navy are the Naval installations around the Bay. † The regulatory community, the federal and state agencies mandated with ensur- ing compliance with environmental laws and regulations. These regulatory agencies include the NMFS, USFWS, US Army Corps of Engineers (USACOE), USCG, State Lands Commission (SLC), California Department of Fish and Game (CDFG), RWQCB (San Diego), and CCC. † Agencies sharing jurisdiction of the Bay with the Port and the Navy are the cities of Chula Vista, Coronado, Imperial Beach, National City, and San Diego; state agencies (SLC, CCC, California Department of Parks and Recre- ation [CDPR]); federal agencies (USFWS and SMNWR); and those within the Bay’s watershed (County of San Diego and several other incorporated cities). Welcome to the Plan 1-15 September 2000
  • 63. San Diego Bay Integrated Natural Resources Management Plan † Users of the Bay, including commercial, recreational, and industrial Port tenants and leaseholders; residents; boaters; recreationists; tourists; fisher- men; and others. † The environmental community as voluntary protectors of the Bay’s natural resources. † The scientific community involved with research, analysis, monitoring, and restoration of the Bay’s ecosystem. † General public and community groups. 1.4.2 Intent of Use This Plan should serve as a planning tool, management guide, reference docu- ment and policy strategy for the Navy and Port, as well as other agencies and organizations. Policy Strategy: The proposed cooperative strategy for resolving key manage- ment issues within San Diego Bay is addressed throughout the Plan, but is emphasized in Chapters 4 through 7. Development of these policy recommen- dations by the TOC and NIOC members required a decision-making process based upon consensus, but compatibility with the Navy and Port missions had to be preserved. Through iteration, the groups proposed and refined objectives, decision criteria, and policies until each member was satisfied. Agency require- ments need to be satisfied and the strategy must be acceptable to the owners of the Bay’s tidelands and to the citizenry, resulting in a policy strategy that can then be broadly supported by all involved. Reference Tool: Information provided within the Plan is intended to meet an original need, which was to pull together an accessible ecological database for the Bay. As a reference tool, the Plan offers a synthesis of what we know about the Bay’s biological resources as well as a bibliography of all known biological surveys. Chapters 2 and 3, maps, and several appendices offer information that can be used as an objective reference by everyone. In addition, Chapter 6 pro- poses standardized means for assessing ecosystem health that can be updated periodically and used to guide a long-term monitoring program. The Plan is to be reviewed and approved by the sponsoring decision-makers: the Commander, Naval Bases San Diego and the Board of Port Commissioners. This Plan is intended to be used by the Navy and the Port as guidance for new master plans, project planning, mitigation strategy, compliance monitoring, National Environmental Policy Act (NEPA), California Environmental Quality Act (CEQA), Coastal Zone Management Act (CZMA), and Clean Water Act (CWA) documenta- tion, and daily resource management decisions. It may be used as a springboard for a mitigation banking plan for the Port and Navy. Chapter 7 “Implementation Strategies” identifies potential sources of funding and other support. 1.4.3 Organization Descriptive sections on the current state of ecosystem resources and human use of San Diego Bay are at the beginning of the Plan (Chapters 2 and 3, respec- tively). Within the strategy sections (Chapters 4 through 7), a synthesis of man- agement issues and needs is first provided for each component. Following these findings is the proposed strategy, which includes a means to fill information gaps identified in earlier chapters. 1-16 Welcome to the Plan September 2000
  • 64. San Diego Bay Integrated Natural Resources Management Plan The strategy statements in Chapters 4 through 7 are in a hierarchical format, beginning with broad, long-term statements and ending with specific, short- term methods. Because clear communication is very important, the definitions of the planning terms are described in Table 1-1. Their relationship from broad to specific is depicted in Figure 1-2. Table 1-1. Planning Definitions. Hierarchy Definition Goal Broad statement of intent, direction, and purpose. An enduring, visionary description of where you want to go. A goal is not necessarily completely obtainable. Objective Specific statement that describes a desired condition. Can be quantitative. Should be good for five years or so. Strategy Explicit description of ways and means chosen to achieve objectives. Policy Formally-adopted strategy or decision to carry out a course of action. Task/Activity/ Specific step, practice, or method to get the job done, usually organized sequentially Tactic with timelines and duty assignments. These go out of date quickly and should be updated annually. Broad Goal Objective 1st-Level Policy 2nd-Level Policy 3rd-Level Policy Strategy Tactic Specific Figure 1-2. Relationship of Planning Terms and Strategy, from Broad to Specific. Chapter 6 “Monitoring and Research” synthesizes information needs and pro- poses the means and priorities for filling them. Guidance for implementation is described in Chapter 7 “Implementation Strategies.” 1.4.4 Implementation Implementation is putting the Plan into effect. To be implemented the Plan must first be understandable, practical, and supportable by those who need to imple- ment it. If those criteria are met, then the Plan will need a commitment of intent, time, and, in many cases, money by the implementers and their supporters. A framework for organizing stakeholders and resources is provided in Chapter 7. Welcome to the Plan 1-17 September 2000
  • 65. San Diego Bay Integrated Natural Resources Management Plan Some of the strategy involves specific actions that may need cooperative funding (e.g. habitat monitoring). However, other strategies suggest changes in policy and do not necessarily require direct funding to implement (e.g. biological assessment methods or criteria for habitat protection). Whatever the case, cooperative efforts are essential to ensure the implementation of this Plan. Signature approval by the Navy and Port authorities as well as by other agencies and organizations provides an authority for implementation. 1.4.5 Updating This Plan is intended to be dynamic and, as such, will require revision to remain current and relevant. Its loose-leaf format provides for changing or updating as fre- quently as needed. Entire sections or individual pages can be removed and replaced. New sections can also be appended. Updating would be appropriate, for example, when results of monitoring efforts reveal new insights and a change in strategy. As an INRMP, the Navy has an obligation to review and, as appropriate, update on a five-year basis. A “Plan maintenance” item in the Navy’s and Port’s annual budgets is one method to ensure regular evaluation of the Plan’s progress and need for updating. 1-18 Welcome to the Plan September 2000
  • 66. San Diego Bay Integrated Natural Resources Management Plan Part II: State of the Bay
  • 67. San Diego Bay Integrated Natural Resources Management Plan 2.0 State of the Bay—Ecosystem Resources The structure and function of the San Diego Bay ecosystem and what we do and do not understand about its condition are the subjects of this Chapter. Component by component, the elements that make up the ecosystem are discussed—climate, hydrology, water, sediment, then habitats and the communi- ties that inhabit them. Finally, the state of the ecosystem as a functional whole is presented, along with an assessment of the gaps in our understanding about the state of the Bay. Photo © 1998 Tom Upton. Photo 2-1. South Bay Mudflat Adjoining Northernmost Levee of Salt Works. September 2000
  • 68. San Diego Bay Integrated Natural Resources Management Plan 2.1 Ecoregional Setting A natural, nearly enclosed embayment, San Diego Bay is an exceptional harbor because of its deep entrance and protected conditions. It originated from alluvial plains of the Otay, Sweetwater, and San Diego Rivers. Southern California bays and estuaries are small compared to those along the east coast and elsewhere. San Diego Bay is unusual among the world’s river-dominated estuaries because it receives min- imal freshwater input and has a high evaporation rate, similar to estuaries of South Africa (J. Largier, Scripps Institute of Oceanography, pers. comm.). „ The Bight is a very diverse and The Bay is part of the Southern California Bight (SCB or “the Bight”), a curve in the productive ecological region, southwestern California coastline that extends from Point Conception to just south where temperate and tropical of the Mexican border (Map 1-1). This ecological region is very productive and species overlap. diverse for several reasons. First, for marine animals, this area represents the north- ern end of the range of many tropical species, and the southern end for many tem- perate species. Point Conception marks a sharp break in sea temperatures. Points north are cooler and just south of the Mexican border temperatures become warmer. Second, the Bight is the landfall terminus of the very complex, Pacific Ocean underwater topography—especially when compared to the long, flat shelf extending seaward from the south Atlantic coast. A system of thirteen large and nineteen smaller submarine canyons, as well as offshore islands, provides habi- tat for a full range of species with different depth and temperature preferences. Special communities such as kelp beds add habitat structure in shallow water, fostering a rich species assemblage. „ Embayments in the Bight contain Third, the SCB contains both cool and warm water due to ocean currents mixing from intertidal habitat required by a subarctic and equatorial regions. Sea temperatures fluctuate regularly due to the number of species. This habitat is changing strengths of these currents. These changes are reflected most by plankton scarce in southern California. and to a varying degree are transferred up the food chain. Finally, the Bight’s embayments, including San Diego Bay, contain intertidal habitat required by a number of species, and which is naturally scarce in south- ern California (compared to the east and gulf coasts, for example). These ecolog- ical “edges” are even more limited today due to commercial development in other harbors and estuaries of the Bight, such as the largest one at San Pedro. 2.2 Physical Conditions 2.2.1 Climate and San Diego Bay experiences an average annual rainfall of about 10 inches (in) Hydrography (25 centimeters [cm]), occurring mostly from November through March. Evapora- tion exceeds rainfall throughout most of the year. The regional climate is classified as semiarid, Mediterranean. Winds over the Bay are usually breezy (about 10 knots [kn]), but these have some strong seasonal and diurnal cycles. Throughout most of the year, westerly winds pick up in the afternoon as cool air moves inland; evening and early morning easterly winds occur primarily in winter and are less than 10 kn (Wang et al. 1998). Stronger winds may occur in winter, associated with cold fronts moving through the region. Easterly Santa Ana winds may be quite strong in the fall, driven by high pressure over inland deserts. Winds are generally greater south of the Coronado Bridge than north of it, with greatest wind speeds in central south Bay, west of Sweetwater Channel (Lapota et al. 1993). 2-2 State of the Bay—Ecosystem Resources September 2000
  • 69. San Diego Bay Integrated Natural Resources Management Plan „ Productivity of the Bay is depen- The combination of nutrient sources, vertical nutrient gradients, warm spring– dent upon the source and vertical summer temperatures, and the attenuation of light with depth in San Diego Bay stratification of nutrients and the is fundamental to its productivity. attenuation of light with depth. The Bay is 15 miles (mi) (24 kilometers [km]) long and varies from 0.2 to 3.6 mi (0.4 to 5.8 km) in width. It is about 17 square miles (mi2) (43 square km [km2]) in area at mean lower low water (MLLW) (Wang et al. 1998). A sand spit, deposited by a northward-bound eddy of the coastal current on the west, separates the Bay from the sea. Historically, the sand transported in this way was laid down from deposition emanating from the Tijuana River. However, since the damming of the river in 1937, the sand supply has been cut off and northern beaches have undergone severe erosion (Peeling 1975). Zuniga Jetty, which runs parallel to Point Loma at the Bay’s inlet, was built to control erosion near the inlet, chang- ing the Bay’s hydrodynamic characteristics by diverting both northward-bound sediment and currents (Wang et al. 1998). Broad lowlands extend about 1.5 mi (2.4 km) south and east from the bay, before rising up into the coastal terrace, or mesa, that supports urban San Diego. Rugged Point Loma hooks around the north side, cutting off the ancient floodplain of the San Diego River, which throughout its evolution alternatively drained into San Diego or Mission Bays. „ The Bay has always had a narrow, With a water volume of about 230,000 cubic meters (m3) (Peeling 1975), the Bay’s natural channel deepening at the depth ranges from 59 feet (ft) (18 meters [m]) near the mouth to less than 3 ft (1 m) mouth. Its area has been reduced at the south end. It has an average depth of 21 ft (6.5 m) measured from mean sea and depth increased over the past century due to dredging and filling. level (Wang et al. 1998). There has always been a narrow, natural channel deepen- ing at the mouth, possibly cut by river floods at a time when sea level was much lower (Peeling 1975). This channel has been and continues to be deepened by dredging for safe passage of ships seeking sheltered anchorage at port. Prior to major filling activities, which began in 1888 and intensified just before and during World War II, the Bay had an area of 21 to 22 mi2 (54 to 57 km2), as defined by the mean high tide line of 1918. About 6 mi2 (15.5 km2) of the Bay has been filled based on this high tide line, or about 27% (Smith 1976). Map 2-1 shows the recent topography of the Bay floor, while Map 3-1 shows the historic habitat breakdown, based on an 1859 chart. Note the natural channel in Map 3-1. Map 2-2 shows the cumulative history of dredge and fill activity. Only 17 to 18% of the original Bay floor remains undisturbed by dredge or fill (Smith 1976). „ Inflow of fresh water into the Bay Freshwater contribution comes primarily from the Otay and Sweetwater Rivers, but estuary comes from seven streams also Telegraph Canyon (south of Sweetwater River Basin), Chollas (north end of Naval and surface drainage. Historically Depot south of NASSCO), Switzer (Tenth Ave. Marine Terminal [north end]), Paleta intermittent, streams now have about 3/4 of their flow diverted (7th Street Channel, south of Naval Repair Base), and Paradise (south of Paleta) Creeks, before reaching the Bay. as well as some minor drainage groups (Map 1-3). The first major reduction of freshwa- ter input occurred when the USACOE diverted the San Diego River to Mission Bay in 1875. Later construction of dams and extensive groundwater use in the Sweetwater and Otay drainages reduced the already ephemeral input from those rivers by 76% (US Army Corps of Engineers 1973). Freshwater input is now limited to surface drain- age from urban areas and intermittent flows from several rivers and creeks after storms. For about nine months of the year, the Bay receives no significant amount of fresh water. Evaporation approximately balances the freshwater input from all sources over the course of the entire year (Lackey and Clendenning 1965). During the sum- mer, however, the evaporation rate of 62.7 in (159 cm)/year in south Bay is higher than precipitation and freshwater inflow (Peeling 1975; Lenz 1976). This can cause south Bay to become hypersaline, or saltier than seawater, in excess of 35% in dry sea- sons (Wang et al. 1998). State of the Bay—Ecosystem Resources 2-3 September 2000
  • 70. San Diego Bay Integrated Natural Resources Management Plan 2.2.2 Sediment Physical parameters, such as characteristics of the sediment, can explain the distri- bution and abundance of organisms, and sometimes changes in biotic populations that are closely tied to substrate. Sediment characteristics reflect hydrodynamic regimes and can also explain the fate and loading of contaminants. Map 2-3 shows percent fine sediments (silt and clay) on the Bay floor (593 data points compiled by Space and Naval Warfare Command [SPAWAR] from several sources). Without human intervention, San Diego Bay would have eventually, in geologic time, filled up with sediment delivered by the San Diego, Otay, and Sweetwater Rivers. In addition, it is likely that the northward drift of beach sand that connected Coro- nado Island with the mainland, and Coronado and North Islands together, eventually would have blocked or nearly blocked the harbor entrance. Breakwaters, channel maintenance, and tidal action prevent this from occurring (Norris and Webb 1990). „ Mud layers on top of sand and Historically, the Bay floor and margins were characterized by sand, silt, clay, mud sandy-silt along the eastern mar- (silt and clay less than 62 microns in diameter), and mudstone. Sands were most gins are removed during dredg- common at the mouth and along the western margins, while finer mud deposits ing, causing the sandier layers to be exposed. characterized the eastern margins and southern extremity of the Bay (Peeling 1975). According to studies in 1980 by the San Diego Gas & Electric Company (SDG&E), thickness of Bay floor muds average 0 to 7.8 ft (0 to 2.4 m). The mud sets upon layers of sand and sandy-silt, then on older semiconsolidated sedi- ments. Dredging exposes these sandier layers. „ The diversion of the San Diego Present contribution of sediment from all potential sources is minimal. As River and the damming of the described above for freshwater inflow, the major historic contribution of sedi- Sweetwater and Otay Rivers has ment was from the three major rivers plus smaller streams, which drained an significantly reduced sedimenta- tion sources into the Bay. area of about 900 mi2 (2330 km2). The current drainage area is 433 mi2 (1122 km2), since diversion of the San Diego River (Table 2-1). The total fluvial sedi- ment delivered to the Bay was on the order of 0.8 to 1.1 x 106m3 per year (Smith 1976). The San Diego River, alone, was estimated to have delivered about 3.8 to 5.3 x 105m3 to the Bay annually (Smith 1976). As evidenced from the promi- nence of the San Diego River and other deltas, fluvial sediment was gradually fill- ing the Bay until the late 1800s. The diversion of the San Diego River ended all sediment deposition from that river, and damming of the Sweetwater and Otay Rivers reduced sediment delivery by 75% (Smith 1976). The present-day sedi- ment contribution from the undammed portions of the remaining drainages is estimated to be about 1.4 to 1.9 x 105m3 per year (Smith 1976). Table 2-1. Estimated trends in total fluvial sediment delivery to San Diego Bay (Smith 1976). Drainage Area Annual Volume of Sediment Drainage Extent (km2) Delivery (m3) Original 2330 800,000–1,100,000 Current (with San Diego River diverted, dams 1122 140,000–190,000 on Sweetwater, Otay, and other drainages) „ Shoreline erosion is a minimal Some sedimentation would be expected from wave erosion of the Bay’s shorelines. contributor of sediment to the However, well over half of the shoreline is protected by piers, docks, bulkheads, Bay because of the amount of revetments, and riprap. The remaining unprotected shoreline is predominantly mooring and low potential for erosion of the remaining sites. on the lee side of prevailing winds (the western shoreline). As a result, only about 18 to 20% of the unprotected shoreline and 7% of the overall Bay shoreline appears subject to significant erosion; therefore, unprotected shoreline is a mini- mal potential contributor of sediment to the Bay (Smith 1976). 2-4 State of the Bay—Ecosystem Resources September 2000
  • 71. San Diego Bay Integrated Natural Resources Management Plan Map 2-1. Recent Topography of San Diego Bay Floor. State of the Bay—Ecosystem Resources 2-5 September 2000
  • 72. San Diego Bay Integrated Natural Resources Management Plan Map 2-2. Cumulative History of Dredge and Fill Activity in San Diego Bay. 2-6 State of the Bay—Ecosystem Resources September 2000
  • 73. San Diego Bay Integrated Natural Resources Management Plan Map 2-3. Percent Fine Sediments (Silt and Clay) on the Bay Floor. State of the Bay—Ecosystem Resources 2-7 September 2000
  • 74. San Diego Bay Integrated Natural Resources Management Plan „ Maintenance dredging needs are During the century prior to the 1960s, when more rigorous regulation went into relatively low due to the severely effect, the annual dredging rate averaged 3.3 to 4.7 x 106m3, which is three to six reduced sediment input to the Bay. times the former yearly sediment input. This annual dredging rate is roughly sev- enteen to 34 times the current yearly sediment input to the Bay. The severely reduced sediment input to the Bay is further confirmed by the unusually low vol- ume of maintenance dredging conducted in interior channel areas (Smith 1976). 2.2.3 Water 2.2.3.1 Turbidity Waters of the Bay become more turbid, or less transparent, as distance increases from the entrance. In the shallow, wider south end of the Bay, where a longer fetch is possible, persistent wind and wave action cause a marked increase in tur- bidity during the winter and early spring. The wind is able to scour up the finer sediments of this region at that time of year. Water is then clearer in the fall months (Lapota et al. 1993). 2.2.3.2 Circulation, Circulation of ocean currents outside the Bay affects organisms having access and Temperature, and Salinity entry to the Bay. The ebb and flood of tides within the Bay circulate and mix ocean and Bay waters, and also transport organisms, especially plankton, in and out of the entrance. Tides produce currents, induce changes in salinity, and alternately expose wet portions of the shoreline. Tidal flushing and mixing are important for dispers- ing pollutants, maintaining water quality for marine life, and moderating water temperature that has been affected by exchange with the atmosphere or heating, such as by the south Bay power plant. „ Tidal exchange in the Bay exerts Bay circulation may be driven by wind, tides, temperature, and density gradients control over the flushing of con- associated with seasonal, tidal, and diurnal cycles. In San Diego Bay, circulation taminants, transport of aquatic is primarily related to tides, because winds are of mild magnitude and there is a larvae, salt and heat balance, and residence time of water. low fetch area (Wang et al. 1998). Tidal patterns off this coast are mixed, with two unequal highs and lows each day. The diurnal difference in the high mean higher high water (MHHW) and low MLLW tides is 5.6 ft (1.7 m), with extremes of 9.8 ft (3 m) (Largier 1997). The tidal prism, or the volume of water contained between the tides, is about 73 x 106 m3 (Gautier 1972). Highest tides are in Janu- ary and June. Tidal exchange in the Bay exerts control over the flushing of con- taminants, transport of aquatic larvae, salt and heat balance, and residence time of water (Chadwick 1997). „ Tidal velocity decreases Tidal current velocities range from 0.6 to 2.7 ft/sec (0.2 to 0.8 m/sec) at the with distance from the mouth (Gartner et al. 1994) to much lower in central and south Bay. Velocities at Bay’s mouth. depth lead velocities at the surface during flood tides by 30 to 90 minutes (Chad- wick et al. 1996). Variations in velocity are due to variations in depth and width of the Bay as the tidal prism moves southward, the presence of side traps such as marinas and basins, and the general reduction in velocity with distance from the entrance (Largier 1997). Longitudinal tidal currents will still, however, exceed the strength of wind and wave action, except during periods of high winds (Fal- ter 1971; SDG&E 1980). „ Thermal gradients are common in Temperature and density gradients, both with depth and along a longitudinal the summer but absent in the cross-section of the Bay, drive tidal exchange of Bay and ocean water beginning winter due to wind and cooling. in the spring and continuing into fall. The seasonal thermal cycle has an ampli- tude of about 46 to 48° F (8 to 9° C) (Smith 1972). Maximum water temperatures 2-8 State of the Bay—Ecosystem Resources September 2000
  • 75. San Diego Bay Integrated Natural Resources Management Plan occur in July and August, and minimums in January and February. In the winter, thermal gradients are absent, with cooler air temperatures and higher winds causing the Bay to be nearly isothermal (Smith 1972). During 1993 surveys, the warmest temperature was 84.7° F (29.3° C) in south Bay, and the coolest temper- ature, 59.2° F (15.1° C), was just north of the Coronado Bridge in January (Lapota et al. 1993). The average surface temperature is estimated to be 63.3° F (17.4° C) (Smith 1972). Smith (1972) also found maximum vertical temperature gradients of about 0.3° F/ft (0.5° C/m) during the summer. Typical longitudinal tempera- ture range is about 45 to 50° F (7 to 10° C) (about 0.3 to 0.5° C/km) over the length of the Bay (Largier 1995) during the summer. Temperature inversions also occur diurnally due to night cooling. „ Salinities in south Bay are greater Salinities near the Bay entrance approach those of the nearby open ocean (31.2 to than in the ocean in late summer, 31.4 practical salinity units [psu] [Largier 1997]). In contrast, south Bay evapora- but can be lower in the winter fol- tion and poor flushing produce salinities as high as 37 psu in late summer (Ford lowing rain and runoff. 1968; Ford and Chambers 1973), decreasing to lows of 22 psu following heavy rains (Largier 1997). This summer occurrence of hypersalinity in south Bay may lead to stratified, density-driven flushing in the fall. This process moderates the build up of hypersaline conditions in south Bay (Largier 1997). Within tidal cycles, the temperature stratification builds up during the flood tide and weakens with the ebb tide. The thermal exchange that occurs at the mouth of the Bay when sea water is mixed with warmer Bay water is complicated by salt gra- dient-driven flows of south Bay water seaward, beneath the less dense water of the surface. As described above, the importance of this stratification depends on the state of the tide, the strength of the wind, and time of year. Estimates of the tidal exchange ratio at the Bay entrance (the proportion of water coming in the Bay with the flood tide that is new oceanic water versus recycled Bay water) range from 0.5 to 0.7 (Fischer et al. 1979; Largier 1995; Chadwick and Largier 1997). „ The Bay’s flushing rate has been The marked reduction in area of the Bay from its historical dimensions has reduced reduced due to the reduction in the volume of the tidal prism by roughly 25%, and it is probably this reduction com- the tidal prism volume and bined with increased depth that has reduced the flushing rate (Smith 1976). Another increased depth. estimate of this reduction is 30% (Browning et al. 1973), while Largier (1997) places it as 33% the volume of the tidal prism. It is also likely that the Bay’s circulation pattern has been modified by this change in geometry (Smith 1976). 2.2.3.3 Residence Time Flushing rates change drastically as one moves away from the Bay entrance. Long- of Water est residence times are observed in the summer, apparently related to the density stratification of the Bay at that time (Chadwick 1997). The amplitude of the tidal cycle also affects the flushing rate. During a strong tidal cycle, up to 40% of the mean volume of the Bay passes Ballast Point during the ebb flow, at least tempo- rarily residing outside the Bay. During an average tidal cycle, the volume of water leaving the Bay is about 13%. This Bay water mixes with ocean water. During the next flood tide, this mix gets pulled back into the Bay. While the residence time of water near the northern inlet of the Bay is short, it can take from ten to 100 days for water in the Bay as a whole to be exchanged, depending on the tidal ampli- tude. Residence times in south Bay may be twenty to 300 days (Chadwick 1997). State of the Bay—Ecosystem Resources 2-9 September 2000
  • 76. San Diego Bay Integrated Natural Resources Management Plan „ During an average tidal cycle, Taking into account this mixing, Map 2-4 shows the half-life of water residing in about 13% of the Bay’s water the Bay with different tidal amplitudes. The actual process is somewhat more leaves the Bay and mixes with complicated, with warm, less dense water moving out of the Bay as a jet near the ocean water before returning on the next tide. surface. Colder, denser water moves in as a front at greater depths. The data are based on a two-dimensional hydrodynamic model (depth is not considered), validated with salinity and temperature correlations (data and graphics provided by Don Sutton and John Helly of the San Diego Supercomputer Center). 2.2.3.4 Hydrodynamic Based on the factors described above, Largier (1996, 1997) described four hydro- Regions of the Bay dynamic regions of the Bay: 1. Marine Region. Circulation in the marine region is dominated by tidal exchange with the ocean. In San Diego Bay, this area of efficient flushing is within perhaps 3 to 4 mi (5 to 6 km) of the entrance, reaching almost to downtown. Residence time of Bay water is just a few days. The net result of these circulation patterns in the Bay is the presence of cold, clean ocean water at depth, explaining the Mussel Watch Project result that mussels at the mouth of the Bay are the cleanest in the county (Largier 1996, 1997). (See Section 2.8.2 “What We Currently Understand About Bay Ecosystem Health” for more on Mussel Watch.) 2. Thermal Region. In the thermal region, still in north Bay but extending to approximately Glorietta Bay, currents are driven primarily by surface heating. The vertical exchange of water results from entry of a cold, oce- anic plug at depth with the flood tide, then the receding of warm, Bay sur- face water with the ebb tide. 3. Seasonally Hypersaline Region. Between about Glorietta Bay and SMNWR is a seasonally hypersaline region. Water is stratified by salinity gradients induced by evaporation. 4. Estuarine Region. South of the SMNWR is an estuarine region where occasional inputs of freshwater discharge from the mouth of the Otay and Sweetwater Rivers. Residence time of Bay water can exceed one month and may approach much longer times in this region. 2.3 Water and Sediment Quality San Diego Bay’s water and sediment quality represents the ecosystem’s chemical and physical properties that reflect the effects of external or human influences. How this quality has changed over time, what the current quality is, and the eco- logical effects of this change, are the topics of this section. 2.3.1 Historical Excellent, detailed accounts of the Bay’s historical water quality problems and Conditions changes can be found in reports by Macdonald et al. 1990 and San Diego Unified Port District 1995. San Diego Bay’s water quality impacts most likely began upon its becoming a harbor in the late 1700s. Until the mid-20th century, its waters were seen as the solution for the disposing of bilge water, garbage, and sewage. Waste disposal of collected sewage into the Bay was first attempted in 1887–1888 when the City’s population was less than 16,000 (San Diego Regional Water Pollution Control Board 1952). Industrial wastes were mainly from the food processing industry in the early part of this century. In 1924, high bacterial levels (ten E. coli organisms 2-10 State of the Bay—Ecosystem Resources September 2000
  • 77. San Diego Bay Integrated Natural Resources Management Plan Map 2-4. Half-life of Water residing in the Bay with Varying Tidal Amplitudes, taking into Account mixing of Bay Water with Ocean Water during Tidal Cycles. The Data are based on a Two-Dimensional Hydrodynamic Model (depth not considered), validated with Salinity and Temperature Correlations. Data and Graphics provided by Don Sutton and John Helly of the San Diego Supercomputer Center. Legend on Graph says “Hours for 50% dilution.” State of the Bay—Ecosystem Resources 2-11 September 2000
  • 78. San Diego Bay Integrated Natural Resources Management Plan per milliliter [ml] or greater) were detected in a zone near the city sewer outfalls but did not extend beyond the pier head into the navigation channel. Before the first sewage treatment plant was constructed by the City of San Diego in 1940, high coliform counts indicated sewage contamination in all parts of the Bay. However, rapid population growth during and after World War II overwhelmed the capacity of the few sewage plants, which used primary treatment and usually no chlorination. „ Until 1952, the Bay was thought By 1952, at least 50 million gallons of sewage and industrial wastes were dis- capable of absorbing all untreated posed of daily into San Diego Bay. Large sections of the Bay were reaching waste sewage and industrial wastes. loading capacities and the Bay was being doubted as “a satisfactory and econom- ical solution to the metropolitan sewage disposal problem” (San Diego Regional Water Pollution Control Board 1952). The San Diego Regional Water Pollution Control Board (SDRWPCB), a newly formed state agency at that time, undertook a comprehensive pollution survey of the Bay that was the first one of its kind on the west coast (Delaney 1966). It identified principal waste discharges to be from three municipal sewage plants’ primary effluent, four industrial sources of untreated wastes, and two military sources of crude sewage. In addition, 4,000 vessels used the harbor every month. „ Sewage solids were commonly Water quality conditions in the early 1950s were indicative of such a large waste found along Coronado’s bayside loading (San Diego Regional Water Pollution Control Board 1952). Visually, the shore, with the east and central color of the Bay’s water varied from green to brown, with widespread oil slicks bays exceeding state health stan- dards in the early 1950s. commonly found, and transparency as low as 2.5 to 5.9 ft (0.76 to 1.8 m) at the industrial east shore. Solid wastes dumped into the south Bay were deposited by wind onto western beaches of the Bay and sewage solids were frequently observed along Coronado’s bayside shore. Coliform bacteria densities were 70 mpn (most probable number)/ml along the east shore and 24 to 70 in (70 to 178 cm) in the central Bay, exceeding California Department of Public Health (CDPH) standards; all recreational areas had high bacterial densities. Dissolved oxygen levels were frequently found to be under 5.0 parts per million (ppm) over most of the south and central areas of the Bay, approaching the then minimum allowable level of 4.0 ppm. „ A large area devoid of bottom Benthic animal life was almost completely absent from a zone 27,001 ft (8,230 m) living organisms was found along by 600 ft (183 m) between the USCG station and the south end of the US Naval the eastern shore due to thick Supply Base due to the lethal effect of up to 3 ft (1 m) of sludge deposits on marine sludge deposits. invertebrates. Toxic wastes were not measured at the time, though industrial oper- ations were known to discharge cyanide, chromium, and other toxic materials and had probably caused a die-off of some birds and cockles in the south Bay in spring 1952. Hydrogen sulfide was dominant in and around Los Chollas Creek, symptomatic of depleted oxygen levels. „ A quarantine was placed on the By 1955, the CDPH found that the waters of the central portion of the Bay had central Bay beaches by the state in deteriorated since 1951 and were now “sufficiently contaminated by sewage 1955. By 1964, all domestic sew- wastes to be hazardous to public health,” particularly for recreational uses (Cali- age was taken to a new sewage treatment plant at Point Loma fornia Department of Public Health 1955). In December, CDPH placed a quaran- and discharged offshore. tine on the beaches and shorelines in the central Bay area (San Diego Unified Port District 1995). The SDRWPCB adopted its first water quality criteria for San Diego Bay that same year. By 1963, dissolved oxygen levels had dropped to 4.0 ppm in all parts of the Bay except at the entrance, with some samples recording 1.0 ppm (Terzich 1965). Finally, in August 1963, the San Diego Metropolitan Sewerage System went into operation and by February 1964, all domestic sewage 2-12 State of the Bay—Ecosystem Resources September 2000
  • 79. San Diego Bay Integrated Natural Resources Management Plan discharges and those from the Naval Amphibious Base (NAB) were connected (Delaney 1966). Treated effluent from this system was, and continues to be, dis- charged through an ocean outfall off of Point Loma. „ Improvements in water clarity and Once the sewage discharges stopped, water clarity improved to 15 ft (5 m) by March marine life became apparent 1964 (San Diego Unified Port District 1995). By 1966, SDRWPCB staff were noticing almost immediately. large schools of fish and occasionally seals in the central Bay (Delaney 1966). Through the return of dissolved oxygen levels in excess of 5 milligrams per liter (mg/l) throughout the Bay, agency staff claimed that about 9,600 acres (3,885 hect- ares [ha]) or 80% of the Bay had returned to being suitable habitat for marine life. Sportfishing and clamming were once again a popular activity. Sludge deposits over 11.8 in (30 cm) deep were seldom found in the original “dead zone,” then shrunken to about 8,999 ft (2,743 m) by 299 ft (91 m) in size. Only a few sites had coliform densities occasionally approaching 10 mpn/ml. The biological oxygen demand, sus- pended solids, phosphate, and nitrogen loadings showed great improvement due to the significant decline in wastes discharged into the Bay, as shown in Table 2-2 below (Delaney 1966). Table 2-2. Comparison of Known Wastes Discharged into San Diego Bay, 1955 and 1966. Volume Biological Oxy- (million gal- gen Demand Suspended Solids Phosphate Nitrogen Year lons /day) (kg/day) (kg/day) (kg/day) (kg/day) 1955 44.28 35,834 45,995 6,305 7,394 1966 2.87 16,352 22,770 240 576 % reduction 93.5 54.5 50.5 96.2 92.2 „ The mid-1960s focused on After this success, attention became focused on the impacts of wastes discharged addressing vessel and industrial from vessels and from industrial sources (Terzich 1965; Delaney 1966; US Federal pollution sources. Water Pollution Control Administration 1969). Vessel discharges from the Bay’s commercial and government ships, as well as party boats and pleasure craft, were specifically evaluated in a comprehensive federal study, which determined that their wastes created conditions “hazardous to health, aesthetically offensive and damaging to ecological balances in San Diego Bay” (US Federal Water Pollution Control Administration 1969). The Naval Station (NAVSTA) area had the highest coliform levels in the Bay, which were twice the standard. Oil spills, primarily from Naval fueling and fuel transfer operations, were noted as another problem. After 1967, industrial dischargers were required to reduce the amount of biolog- ical oxygen demand and settleable solids to meet SDRWPCB discharge require- ments. Storm drains were also identified as sources of chemical and bacteriological contaminants to the Bay in 1965, but no estimate was made of their discharge volume or content. „ The Navy had stopped all vessel By 1969, water quality conditions for turbidity, salinity, transparency, nutrients, and industrial discharges to the and associated plankton populations were generally within the limits set forth Bay by 1980. by the State-Federal Water Quality Standards in most parts of the Bay (US Federal Water Pollution Control Administration 1969). In 1971, San Diego Bay was reportedly considered “one of the world’s cleanest metropolitan bays” (San Diego Unified Port District 1995). The Navy began eliminating vessel discharges in the early 1970s and ceased all ship sewage and industrial waste discharges into the Bay by 1980 (San Diego Unified Port District 1995). State of the Bay—Ecosystem Resources 2-13 September 2000
  • 80. San Diego Bay Integrated Natural Resources Management Plan „ Contamination from heavy metals San Diego Bay’s bacterial contamination from sewage discharges overshadowed the and toxicants started gaining issue of other possible contaminants for decades. In the 1970s, staff from the RWQCB, attention in the 1970s. San Diego Region, began to take notice of industrial wastes and high levels of heavy metals and toxicants within the Bay (Mathewson 1972; California Regional Water Quality Control Board 1972). Much of the chemical pollution was found in the Bay’s sediment rather than in the water column. A series of studies showed San Diego Bay to have serious problems with chemical pollution, even though the conditions were similar to other urbanized bays (California State Water Resources Control Board 1976; California Regional Water Quality Control Board 1985; Kennish 1997). „ High levels of copper, TBT, PCBs, Copper ore spills and associated discharges at a copper loading facility at the 24th and PAHs were detected in the Street Marine Terminal caused concentrations in bottom sediments in the spill area Bay’s sediments in the 1980s. to be 25 times higher in the mid-1980s than prespill levels (California Regional Water Quality Control Board 1985). In that same decade, tributyltin (TBT) levels were found to be very high in marinas and commercial and Naval ship basins where antifouling hull paints were concentrated (Valkirs et al. 1991). In the 1984 National Status and Trends Program (NS&T) for Marine Environmental Quality measured polychlorinated biphenyls (PCBs) at 422.10 parts per billion (ppb) in San Diego Har- bor and 6.74 ppb in San Diego Bay, while polycyclic aromatic hydrocarbons (PAHs) measured 5000.00 ppb near Harbor Island and 0.00 at the Coronado Bridge (National Oceanic and Atmospheric Administration 1987 in Kennish 1997). Over- all, San Diego Bay was ranked 5th in the nation for total PCBs in mussels and 10th for PAHs in mussels during the 1986–1988 national Mussel Watch Project out of about 145 in estuaries, embayments and open coastal sites (Kramer 1994; National Oceanic and Atmospheric Administration 1989 in Kennish 1997). „ San Diego Bay ranked 5th in the Sediment quality had also changed due to the influx of upstream sediments nation for total PCBs in mussels from the Sweetwater and Otay Rivers during very large storm events. In the win- for the period 1986–1988. ter of 1980, a large amount of sediment was flushed into the south Bay because of spill-overs at upstream reservoirs. Total organic nitrogen concentrations gen- erally decreased over the area’s sediments, along with an increased coarseness in grain size (Lockheed 1981 in Macdonald et al. 1990). 2.3.2 Current Conditions Present day water quality concerns for San Diego Bay focus mainly on the quanti- ties of contaminants found in the sediments, shellfish, and other marine organisms (Lapota et al. 1993). Monitoring studies and research are continuing to seek answers to the many questions about the Bay’s water and sediment quality condition. The entire San Diego Bay is listed as an impaired water body (under Clean Water Act (CWA) Sec. 303[d]) by the California State Water Resources Control Board (SWRCB) due to benthic community degradation and toxicity. Some ecological effects of impaired water quality are discussed in Section 2.3.4 “Ecological Effects”. 2.3.2.1 Contaminants Contaminants that are currently of concern in San Diego Bay include: † chlordane (total) † chromium † copper † mercury † TBT † zinc † PAH compounds † PCBs (total) 2-14 State of the Bay—Ecosystem Resources September 2000
  • 81. San Diego Bay Integrated Natural Resources Management Plan „ A recent state assessment found As part of California’s ongoing Bay Protection and Toxic Cleanup Program, San the Bay to exceed threshold qual- Diego Bay’s sediment was evaluated for chemical and biological conditions between ity values for six constituents, and October 1992 and May 1994 (Fairey et al. 1996). Results indicated chemical pollu- identified priority toxic sites. tion based on established sediment quality guidelines, developed by National Oce- anic and Atmospheric Administration (NOAA) and the State of Florida and used as a substitute for absent US Environmental Protection Agency (EPA) and California guidelines. Major chemicals or chemical groups most often found to exceed thresh- old quality values were copper, mercury, zinc, total chlordane, total PCBs, and the PAH compounds. Seven stations (representing four sites) in this Program were given high priority ranking based on toxicity, chemical and benthic community data: Sev- enth Street channel area, two Naval installation areas near the Coronado Bridge, and the downtown Anchorage area west of the airport. Forty-three stations were given a moderate priority ranking, mostly commercial and Naval installation areas in the vicinity of the Coronado Bridge. „ PAHs may be the least understood PAH pollutants are organic compounds that are among the heaviest molecular frac- organic compounds but are tion of petroleum hydrocarbons (Woodward-Clyde 1996). Because they are not very known to be long lived in marine soluble in water and tend to accumulate as particulates in aquatic systems, they can sediments, becoming concen- trated in the food chain. become persistent as well as concentrated within the aquatic food chain. Com- monly found at high levels in estuarine and marine sediments near industrial cen- ters, they serve as a continual source of contamination for biotic communities (Kennish 1997). PAHs are released through fossil fuel combustion, asphalt produc- tion, leaching of creosote oil, and spills of oil, gasoline, diesel, and other petroleum products. An overall criticism of the available literature on PAHs is the absence of enough high quality data to estimate mass loadings. Ultra-low PAH detection meth- ods are necessary, yet there is still a major void in knowledge on atmospheric fallout of pyrogenic PAHs and the pathways to receiving waters (P. Michael, California Regional Water Quality Control Board, pers. comm.). „ Bay sources of copper are mainly Recent studies evaluated the sources of two contaminants, copper and PAHs, for San from the leaching or in-water Diego Bay (PRC 1996; Woodward-Clyde 1996). While not peer-reviewed, these stud- cleaning of copper-containing ies suggest the relative amounts estimated to come from various sources (Figures 2-1 antifouling paint on ship and boat hulls. PAHs in the Bay appear to and 2-2). Copper’s major origin appears to derive from ship and boat hulls (77%), primarily come from the leaching with the leaching of copper-containing antifouling hull paints the primary cause of creosote from pier pilings. and in-water hull cleaning the secondary cause. In contrast, PAH origins are the leaching of creosote from pier pilings in the Bay (61%), followed by in-place sedi- ments introduced to the water column, mainly through dissolved molecules (27%). 0.6 5.6 6 Hull paint leaching 11.2 In-water hull cleaning 42.7 Wet/dry weather flows Sediment to water transfer Ship and boat yards Other 33.9 Figure 2-1. Percent Total Copper Loading to San Diego Bay. State of the Bay—Ecosystem Resources 2-15 September 2000
  • 82. San Diego Bay Integrated Natural Resources Management Plan 3.5 8 Creosote leaching Sediment (sed + water) 27.5 Oil spills Atmospheric 61 Urban runoff (<1%) Industrial runoff (<1%) Figure 2-2. Percent Total PAH Loading to San Diego Bay. „ A 1997 survey revealed improved The Navy measured PAH and copper concentrations in 1997 to assess the effects of PAH levels in the Bay and signifi- its recent changes in bilge water operations and the removal of creosote impreg- cantly lower levels at the Naval nated pier pilings at NAVSTA (US Department of the Navy 1998). Total PAH con- Station. The Navy attributes the reduction to removal of creosote centrations ranged from 24 to 200 micrograms per liter (µg/l) during two surveys, pilings and changes in bilge water reaching maximum levels near NAVSTA. Sources of PAH appeared to be from operations. weathered creosote and fuel product sources. Copper concentrations ranged from 0.41 to 4.18 µg/l. Increased copper levels were found in semienclosed basins and at NAVSTA. PAH levels were the lowest measured in the Bay in the past eight years, and significantly lower by a factor of nine at NAVSTA sites, which was attributed to the operational changes by the Navy there. However, copper levels at NAVSTA were not significantly lower, though the remainder of the Bay had significantly lower copper concentrations. „ TBT levels in the Bay have Levels of TBT, formerly a serious problem in the Bay’s marinas, have decreased sig- declined since their restriction but nificantly since this component of antifouling paints was restricted to Navy ships in chlorane levels have not. PCB pol- 1988 (Valkirs et al. 1991). TBT also naturally degrades to tin. However, TBT still lution remains a prominent prob- lem along the eastern and remains a serious concern in areas of high vessel density and low hydrologic flush- northern waterfront. ing (California Regional Water Quality Control Board 1994). Sediment concentra- tions at commercial and Naval basin areas have declined but are still higher than other areas in the Bay (Fairey et al. 1996). PCBs are extremely persistent in the environment and can cause various carcino- genic and adverse effects to marine life and people. Total PCB pollution was most prominent in sediments along the Naval installation waterfront as well as several locations along the downtown waterfront and small boat harbors. Chlordane, an insecticide discontinued in the mid-1970s, has caused extensive contamination along the north shore of the Bay and in areas receiving storm runoff (Fairey et al. 1996). „ Bioconcentration of certain con- Since several pollutants are known to bioaccumulate in the tissues of marine species, taminants in the tissues of marine a tissue contamination study was recommended for PCBs, chlordane, and possibly species is a real concern and methylmercury to determine potential human health problems associated with needs additional study. consuming resident species of finfish and shellfish (Fairey et al. 1996). Contami- nants of uncertain concern in regard to bioaccumulation include tin, cadmium, sil- ver, lead, and organotin. Of these, tin, cadmium, and lead have all been detected at elevated levels in San Diego Bay‘s sediments (Mearns 1992). PAHs are known to be absorbed and to accumulate in marine organisms and have the potential to cause cancer, mutations, and abnormal growth (Kennish 1997). 2-16 State of the Bay—Ecosystem Resources September 2000
  • 83. San Diego Bay Integrated Natural Resources Management Plan „ Contaminated sites are being Contaminant levels are being reduced through sediment remediation projects at cleaned up through remediation priority sites. Since 1990, the Port has removed contaminated marine sediments projects throughout the Bay. from Tenth Avenue Marine Terminal (TAMT), National City Marine Terminal (NCMT), America’s Cup Harbor (ACH), and East Harbor Lagoon (San Diego Uni- fied Port District 1995). Regional Board Cleanup and Abatement Orders require that remaining sediments in boatyards achieve a copper level below 530 ppm and a mercury level below 4.8 ppm. According to the RWQCB, San Diego Region, the following sites have been cleaned up as of September 1998: † PACO Terminals at 24th St. Marine Terminal (copper) † Kettenburg boatyard (copper, mercury, TBT) † Bay City Marine boatyard (copper, mercury, TBT) † Driscoll boatyard (copper, mercury, TBT) † Mauricio boatyard (copper, mercury, TBT) The following sites have cleanup agreements with RWQCB: † Campbell Marine shipyard, † National Steel and Shipbuilding shipyard, and † Southwest Marine shipyard. The following sites were capped: † Teledyne Ryan Aeronautical storm drains (PCBs) † Stennis Ocean Control Carrier (CVN) site (PCBs, copper, zinc). 2.3.2.2 Coliform Coliform contamination of the Bay can become a problem near stormwater out- Contamination falls and streams following rain storms. The first major rainfall of the season con- tributes high levels (Macdonald et al. 1990; San Diego Unified Port District 1995). High levels of bacteria were measured in the 1993–1994 wet weather sea- son at the receiving waters of Chollas and Switzer Creeks (San Diego Unified Port District 1995). Sources of this contamination most likely include leaking or bro- ken sewer lines, illegal dumping of sewage, and domestic animal feces. The County of San Diego has monitored recreational sites in the Bay for indicator bacteria for several years, with many exceedances of state recreational water con- tact standards near storm drains and in poor circulation areas (San Diego Bay Interagency Water Quality Panel 1998). „ Coliform bacteria contaminate The City of San Diego’s Public Health Department has had to close beaches in recent recreational sites during episodes years due to sewage spills ranging from 1,300 to 3,000 gal (Rodgers 1997). Sewage of sewage spills and stormwater from broken lines enters storm drains and contaminates the Bay during dry weather runoff. Pleasure boats also can dump sewage. as well as wet. Another source of coliform contamination is illegal dumping of sew- age from recreational boats and live-aboard boats. 2.3.2.3 Other Water Quality Nutrient levels compared favorably in 1993 to those from 1980 (Lane 1980; Conditions Lapota et al. 1993). January had the highest concentrations of phosphate (0.2 to 3.1 µg technical atmosphere per liter [at/l], nitrate (12.0 to 31.9 µg-at/l), and ammonia (3.5 to 9.3 µg-at/l). Chlorophyll concentrations ranged from 1.8 to 18.9 µg/l at their highest in January. These levels correlate with maximum algal State of the Bay—Ecosystem Resources 2-17 September 2000
  • 84. San Diego Bay Integrated Natural Resources Management Plan production that month, with measured nutrients higher in south Bay than north Bay. High chlorophyll levels in 1993 were thought to be the result of increased nutrient loading from the freshwater runoff into the Bay. „ The Bay’s watershed contributes With its large watershed, the Bay receives drainage from the cities of San Diego, pollution that causes sediment con- National City, Chula Vista, Lemon Grove, El Cajon, Bonita, Imperial Beach, and tamination adverse to aquatic life. Coronado, and from surrounding communities as far east as the Cuyamaca Mountains (San Diego Unified Port District 1995). Storm drains and streams deliver pollution from many nonpoint sources: automobile oil and grease that build up on roads and parking lots, fertilizer runoff from lawns, illegal dumping of chemicals, yard debris, garbage, and soil erosion. San Diego Bay’s watershed was identified as an Area of Probable Concern by the National Sediment Quality Survey in 1997 because 32 sampling stations showed sediment contamination where associated adverse effects to aquatic life were probable (Tier 1) (US Envi- ronmental Protection Agency 1997). 2.3.3 Regional Within the Bight, a review of the long-term findings reveals that most contami- Comparisons nants increased during the 1950s and 1960s, but decreased during the 1970s and 1980s (Mearns 1992). Metals in fish have not elevated and have not changed, despite significant pollution controls. Pesticide levels are 100 times lower today. Overall, the levels of most pollutants in the open coastal zone are now declining compared to their levels of 30 to 40 years ago. However, sediments of bays and harbors are more contaminated than the open coast. Major gaps are evident in trend monitoring for bays and harbors where “long-term monitoring has been virtually nonexistent,” according to Mearns (1992). „ San Diego Bay continues to rank In a 1987 regional survey, PAHs in sediments collected at southern California among the highest bodies of stations between Santa Monica Bay and San Diego Bay found the Seventh Street water for contaminated sedi- (Paleta Creek) and Chollas Creek stations to contain the highest levels of these ments in California. hydrocarbons of all stations sampled (Anderson and Gossett 1987). Comparing ten coastal sites in southern California, a 1988 study revealed samples from San Diego Bay to have the highest concentrations of metals, PAHs, and hydrocar- bons of all stations sampled and were the most toxic in two out of three toxicity tests used (Anderson et al. 1988). The 1997 National Sediment Quality Survey determined that San Diego Bay, San Francisco Bay, and offshore areas around San Diego and Los Angeles appear to have the most significant sediment con- tamination in the EPA’s Region 9 (US Environmental Protection Agency 1997). „ SCCWRP should provide compara- The Southern California Coastal Water Research Project (SCCWRP) regional moni- ble data among southern Califor- toring effort should be able to provide some valuable comparable data among the nia bays and ports in a few years. various southern California bays and ports in a few years (P. Michael, pers. comm.). 2.3.4 Ecological Effects The effects of the historically high sewage pollution levels on the Bay’s flora and fauna were partially documented in the 1950s and 1960s (San Diego Regional Water Pollu- tion Control Board 1952; Terzich 1965). The CDFG and the Federated Sportsmen of San Diego County reported great changes in the numbers and types of fish and wild- life using the Bay. By 1952, the Bay only supported a few of the “particularly sturdy rough fish,” with no evidence of croaker, corvina, sand bass, halibut, or sea trout and few bait fish. Razor clams, cockles, and scallops had disappeared and migrating water- fowl only used the Bay occasionally for a brief stopover. A die-off of hundreds of ducks, gallinules, cormorants and other shorebirds, and large numbers of cockle clams and fish in the south Bay in the spring of 1952 was attributed to the discharge of toxic 2-18 State of the Bay—Ecosystem Resources September 2000
  • 85. San Diego Bay Integrated Natural Resources Management Plan metal processing wastes (San Diego Regional Water Pollution Control Board 1952). A zone of about 373 acres (151 ha) on the east shore was devoid of benthic invertebrates due to the toxic effects of thick sludge deposits. Laboratory tests by CDFG showed that crabs were more susceptible to the toxic effects than molluscs or worms. „ Sewage pollution devastated the After the regional sewage treatment plant, with its ocean disposal outfall, became fish and wildlife populations of the operational in 1963, the effect of improved water quality on fish and wildlife in the Bay by the 1950s, but their popu- Bay became apparent almost immediately. Observers noted in April 1964 the return lations rebounded rapidly upon improvements in the water qual- to its waters of sculpin, sole, sand bass, octopus, shark, seal, porpoise, bonito, and ity in the 1960s. other fish while returning birds included cormorants, “bluebills,” scoters, and mer- gansers (Terzich 1965). A 1968 study described the south Bay as supporting a diver- sity of marine species representative of the inner sections of relatively undisturbed bays and estuaries in California and Baja California (Ford 1968). However, central Bay and its shoreline still showed the ecological effects of sludge deposits with bot- tom organisms reduced to only a few of the most pollution tolerant species; a pol- luted site was indicated by less than five kinds of organisms or more than 200 polychaete worms per square foot (Parrish and Mackenthun 1968). „ Healthy fish and invertebrate pop- By 1973, the CDFG noted that “healthy fish and invertebrate populations again ulations were noted in 1973 and flourish in many areas,” with eelgrass beds becoming reestablished on dredged sites undesirable algal mats had greatly and ecologically desirable marine plants beginning to grow on pilings and rock reduced. structures (Browning et al. 1973). The “ecologically undesirable” algal mats that had previously covered the bottom of portions of the central and south Bay areas were also greatly reduced. „ Thermal effluent from the south Thermal pollution from the SDG&E south Bay power plant’s discharge was found Bay power plant causes a to cause adverse effects on marine life within 1,801 to 3,901 ft (549 to 1,189 m) of decrease in the number of species the discharge point (Ford et al. 1970). Only marine invertebrate and algae species within the cooling channel during late summer. On the plus side, the tolerant of the temperature conditions were found in this zone, although adverse warmed water increases biomass effects to the Bay outside the cooling channel were determined to be minimal, for some organisms and provides mainly affecting decapod crustaceans and gastropod molluscs. Impacts were year-round habitat for the endan- apparently greatest from the late summer cooling water discharge, with additional gered green sea turtle. species occupying the channel area during cooler periods. Beneficial effects of the thermal plume included significant biomass increases for several major groups and the creation of favorable year-round habitat for the endangered green sea tur- tle (Macdonald et al. 1990). Ecological effects of the thermal effluent on certain marine species at the site were also studied in several master’s theses at San Diego State University (SDSU) (Kellogg 1975; McGowen 1977; Merino 1981). High winter runoff in 1980 caused sediment changes of increased grain size and decreased total organic nitrogen levels in the south Bay. The species composition and benthic community structure of infaunal invertebrates remained very simi- lar to prestorm conditions (Lockheed 1981). „ High copper levels in the Bay The effects of high (>3.0 ppb) and low (<1.0 ppb) copper levels on phytoplank- reduced phytoplankton diversity ton communities in San Diego Bay were studied for one year (Lane 1980). Phy- but have no effect on biomass toplankton samples taken from high copper level areas showed less species or productivity. diversity but maintained high biomass and productivity. The effects of excessive copper levels have been evaluated nationally for various marine organisms: sea anemones, mussels, softshell clams, snails, zooplankton, amphipods, crabs, sandworms, algae, and topsmelt (Atherinops affinis). As a result, copper criteria to protect marine life and human health are proposed in a new federal review of copper hazards (Eisler 1998). State of the Bay—Ecosystem Resources 2-19 September 2000
  • 86. San Diego Bay Integrated Natural Resources Management Plan „ Certain sportfish species in the Bioaccumulation of potentially toxic chemicals by organisms in the food chain is a Bay are known to accumulate concern that is still being studied. One study compared the Bay to nonurban sites PCBs and mercury at levels that and found high concentrations of PCBs in liver tissues of white croaker (Genyone- could pose health risks for con- sumers. mus lineatus), barred sand bass (Paralabrax nebulifer), and black croaker (Cheilotrema saturnum) from several sites (McCain et al. 1992). Barred sand bass showed symptoms of fin erosion. A health risk study of the Bay in 1990 determined that mercury and PCB levels in selected fish species could pose a limited health risk, if significant quantities of fish were consumed. San Diego Bay posed less of a risk than Santa Monica Bay (San Diego County Department of Health Services 1990). The relative quality of the Bay’s benthic invertebrate community was analyzed from 1992–1994 as an indicator of sediment quality and toxicity (Fairey et al. 1996). The results of this study are shown in Map 2-5. The Degradation Index reflects the level of species diversity and the occurrence of opportunistic species that are more toler- ant of high pollution levels. These data, combined with toxicity and chemical data, were used to recommend priority areas for more intense evaluation. 2.4 Bay Habitats „ The water column as a habitat Habitats of the Bay are arranged by depth with respect to the tides, then by sub- is treated under Deep Water, strate, water clarity, and other factors. Figure 2-3 depicts approximate position- although the water column ing of the habitats, defined in this Plan, in relation to tidal elevation, using extends to shallower depths. Also, the benthos as a habitat is dis- Broadway Pier as a reference point. Map C-1 shows the two-dimensional distri- cussed under Unvegetated Shal- bution of these habitats as they occur today. These habitats are linked together low Subtidal, even though it ecologically by the transport of energy and other resources. These relationships extends to deeper depths. are discussed in Section 2.7 “The Ecosystem as a Functional Whole.” The water column as a habitat is treated under Deep Water, although the water column extends to shallower depths. Also, the benthos as a habitat is discussed under Unvegetated Shallow Subtidal, even though it extends to deeper depths. The shallower habitats and the Bay’s natural shoreline have been severely depleted or modified, beginning with the first pier at the end of Market Street in 1850, and the first dredging in 1914. Table 2-3 shows the habitat losses, compar- ing an 1859 geodetic chart and a 1995 aerial photo. 2.4.1 Deep Subtidal Habitat Description (>–20 ft [–6 m] MLLW) Deep subtidal habitat includes the surface water, water column and sediments for areas greater than 20 ft (6 m) in depth, constituting about 4,440 acres (1,797 ha) (34%) of Bay surface area. It is associated primarily with navigational chan- nels. Except for a few areas in north Bay that have no dredging record, all deep subtidal habitat has been dredged since the 1940s; most was dredged in the 1960s or more recently. 2-20 State of the Bay—Ecosystem Resources September 2000
  • 87. San Diego Bay Integrated Natural Resources Management Plan Map 2-5. San Diego Bay Benthic Community Quality Analysis. State of the Bay—Ecosystem Resources 2-21 September 2000
  • 88. San Diego Bay Integrated Natural Resources Management Plan Upland Transition Dunes, Riparian, Freshwater Wetlands, River Mouths, Salt Ponds MHWS +7.8 ft (+2.4 m) Intertidal Approx. Zone of Salt Marsh 1 +7.8 to +2.3 ft (+2.4 to +0.7 m) MHHW +5.7 ft (+1.7 m) Approx. Zone of Beach, Shoreline Stabilization Structures MSL +2.9 ft (+0.9 m) +7.8 to 0.0 ft (+2.4 to 0.0 m) Approx. Zone of Mudflats2 MLLW 0.0 +2.3 to 0.0 ft (+0.7 to 0.0 m) MLWS –2.2 ft (–0.7 m) –3.0 ft (–0.9 m) Shallow Subtidal Vegetated and Unvegetated Estimated lowest use by foraging shorebirds Approx. Zone of Eelgrass 0.0 to –24 ft (0.0 to –7.3 m) depending on water clarity, etc.3 –12.0 ft (–3.7m) Moderately-deep Subtidal Vegetated and Unvegetated MHWS (Mean High Water, Spring): the 19-year average height of high water occurring on spring tides (average during new and full moon days and the 2 days following each). MHHW (Mean Higher High Water): the 19-year average of higher high tides (only in a mixed tidal regime). –20 ft MSL (Mean Sea Level): the 19-year average of hourly water height Deep Subtidal (–6.1 m) (not the same as the fixed geodetic MSL reference point). MLLW (Mean Lower Low Water): the 19-year average of lower low tides (only in a mixed tidal regime). MLWS (Mean Low Water, Spring): the 19-year average height of low water occurring on spring tides (average during new and full moon days and the 3 days following each). Vertical Datum MLLW, Sea Level Datum NOAA Harmonic Station Broadway, San Diego Bay 1998. Source for tidal definitions: Clark 1996 1 Lower limit of salt marsh is defined by lower limit of cordgrass (Spartina foliosa). These tidal elevations are estimated based on salt marshes neighboring those of San Diego Bay. This is as low as +2.3 ft (0.7 m) MLLW in Mission Bay (Levin et al. unpubl. data). In Tijuana Estuary and Anaheim Bay, lower limits range from +3.5 to +5.25 ft (+1.1 to +1.6 m) MLLW (Zedler et al. 1992; Massay and Zembal 1979). 2 Mudflat zone derived from lower limit of cordgrass to upper limit of eelgrass (0.0). 3 In San Diego Bay, depth of eelgrass varies with Bay regions as follows: south Bay 0.0 to –7 ft (0.0 to –2 m) MLLW; central Bay 0.0 to –8 ft (0.0 to –2.4 m) MLLW; north Bay 0.0 to –13 ft (0.0 to –4 m) MLLW. Near the mouth in north Bay, there is a different form (wider blades) that extends down to –18 to –24 ft (–5.5 to –7.3 m) (Hoffman, pers. comm.) Figure 2-3. Habitat Definitions Used in this Plan in Relation to Tidal Elevation. 2-22 State of the Bay—Ecosystem Resources September 2000
  • 89. San Diego Bay Integrated Natural Resources Management Plan Table 2-3. San Diego Bay: Comparison of Current and Historic1 Habitat Acreages Current Acres/Hectares 1859 Acres/Hectares Percent Loss Habitat (depths in feet)2 (% of total) (% of total) or Gain Deep Subtidal (>–20) 4443 / 1798 (28%) 2212 / 895 (12%) +100% Moderately Deep Subtidal 2219 / 898 (14%) 954 / 386 (5%) +133% (–12 to –20) Shallow Subtidal (–2.2 to –12) 3734 / 1511 (24%) 6400 / 2590 (35%) –42% Vegetated Shallow Subtidal3 1065 / 431 (7%) Unknown Unknown Intertidal excluding Salt Marsh 979 / 396 (6%) 6148 / 2488 (33%) –84% (+2 to –2.2 in Map C-1, high tide line to –3 on 1859 coverage) Artificial hard substrate 4,5 45.4 mi / 73.1 km 0 +74% (riprap and seawall; piers, wharves) of shoreline Salt Marsh 823 / 333 (5%) 2785 / 1127 (15%) –70% Upland Transition 2313 / 936 (15%) Unknown Unknown Riparian 7/3 (<1%) Unknown Unknown Freshwater Marsh 1 / 0.4 (<1%) Unknown Unknown Salt Works Crystallizer 121 / 49 N/A N/A Pickling 59 / 24 N/A N/A Primary 462 / 187 N/A N/A Primary/Intertidal 106 / 43 N/A N/A Secondary 366 / 148 N/A N/A Dikes 62 / 25 N/A N/A Total 15694 / 6351 18500 / 7487 –15% 1. Historic figures are based on an 1859 chart. Current figures are based on a 1995 aerial photo taken at Mean Lower Low Water and bathymetry from 1859 versus current chart. 2. All depths based on MLLW. 3. Vegetated shallows is a subset of shallow subtidal, so is not included in the totals. 4. Plus 131 acres (53 ha) horizontal surface structures (piers, etc.). 5. Artificial hard substrate is a subset of subtidal and intertidal habitats, so is not included in the totals. Use of the Habitat „ Except for a few areas in north Bay Deep subtidal habitat is used by a wide variety of vertebrate and invertebrate spe- that have no dredging record, all cies. Some specifically inhabit the open water areas, some spend only part of their deep water areas have been life cycle in the open water, and others use the open water to access coastal areas. dredged since the 1940s; most were dredged in the 1960s or Within the water column are microscopic species of phytoplankton and zoop- more recently. lankton (see also Section 2.5.1 “Plankton”). Their movement and distribution are completely dependent on currents and they are continually flushed out to sea by tides. Phytoplankton are an important primary producer in the Bay. Their bloom appears to be driven seasonally by stormwater runoff, peaking in January (Lapota et al. 1993). Feeding on the phytoplankton and with a potentially completely dif- ferent seasonal cycle are the zooplankton, including abundant meroplankton or “temporary plankton,” the larval forms of invertebrates that later settle to the bot- tom and become benthic juveniles and adults. These forms occur together with species called holoplankton, which are zooplankton that spend their entire lives in the open water environment in planktonic form. The density and diversity of holoplankton are greater in north Bay, which is closer to coastal ocean water (Ford 1968). Some zooplankton migrate vertically through the water column from day to night, as well as horizontally with tidal movement. State of the Bay—Ecosystem Resources 2-23 September 2000
  • 90. San Diego Bay Integrated Natural Resources Management Plan „ Waterbirds use deep water habitat of the Bay, as do fish, sea lions, and dolphins. Occasionally, gray whales visit in the deep water near the Bay mouth. Photo © 1998 San Diego Unified Port District. Photo 2-2. Sea Lions Napping on Buoy. Bay fish surveys found that fish inhabiting open water had numerical and biomass densities which were the lowest of all sampled habitats (Allen 1999). The most com- mon species were the round stingray (Urolophus halleri), California halibut (Paralich- thys californicus), and barred sand bass. Bird abundance and diversity also appears lower in deep water habitats than in shallower ones (US Fish and Wildlife Service 1995a; Ogden 1995). However, many different waterbirds use the open water for feeding and resting. The California least tern (Sterna antillarum browni) and the Cali- fornia brown pelican (Pelecanus occidentalis californicus), both federally listed endan- gered species, forage in the open water, but especially along the Bay margins where schooling fish concentrate. In addition to foraging, brown pelicans use these areas for staging fall migration, roosting, and for juvenile pelicans to scatter in search of new territory (US Fish and Wildlife Service 1997). Ogden (1994) reported many ele- gant and other terns using the open water habitat. Surf scoter (Melanitta perspicillata) make more use of deep water than other birds (Ogden 1995). California sea lions (Zalophus californianus) use buoys in deep water areas for hauling out, and California bottlenose dolphins (Tursiops truncatus) may be seen regularly in the deep water of north Bay. Occasionally, visiting gray whales (Eschrichtius robustus) visit near the Bay mouth. Organisms that live in the deep water benthos have a patchy distribution due to changes in sediment particle size on the Bay floor and to their own reproduction and dispersal mechanisms which have a clumped pattern. Function An important function of the deep water environment is the transport of plank- ton into and out of the Bay for coastal species that depend on access to the warm, sheltered, shallow waters during early life cycle stages. This includes the larvae of many fishes and crustaceans. 2-24 State of the Bay—Ecosystem Resources September 2000
  • 91. San Diego Bay Integrated Natural Resources Management Plan The food web in deep water is dependent upon detrital “rain” from sunlit surface waters. Fungi, bacteria, and protozoans of the benthos help break down coarser organic matter, making it available to higher organisms. As this organic matter is progressively consumed by larger and larger organisms, protein becomes increasingly concentrated up the food chain, creating higher quality food. While most of the deep water benthic habitat is not accessible to birds, benthic organisms do provide forage to rays and flatfishes. They also release planktonic larvae, which frequently undergo diurnal vertical migrations. 2.4.2 Moderately Deep Habitat Description Subtidal (–12 to –20 ft Approximately 2,219 acres (898 ha) (17%) of Bay surface area falls into the moderately [–4 to –6 m] MLLW) deep category, primarily in south-central Bay off the coast of the NAB and in inlets of north Bay. The habitat extends from the approximate lower depth of most eelgrass to the approximate edge of the shipping channel. It represents areas that generally have been dredged in the past but are not maintained as navigational channels. The most recent dredging record at these depths off of NAB is dated 1941–1945. Sediment tex- ture varies widely, from 5 to 95% fines. „ Due to their potential for While it generally supports similar communities to deeper habitat, moderately enhancement, moderately deep deep water habitat is distinguished in this Plan because it represents potential water habitats are distinguished enhancement sites for shoring up to shallower depths, which are more represen- from deep water in this Plan. tative of historical habitat conditions. Use of the Habitat Allen’s sampling scheme for fish abundance and distribution (see also Section 2.5.4 “Fishes”) does not allow quantification of use for moderately deep water habitats with the definition used in this Plan (deep, moderately deep, and one shallow area were lumped by Allen into a single “channel” category). Allen’s open water and offshore sampling locations fell into three depth categories using the definitions of this Plan: deep (north and north-central Bay), shallow (south-central Bay), and moderately deep (south Bay). The moderately deep, south Bay region is dominated by round stingray, spotted sand bass (Paralabrax maculatofasciatus), California halibut, and barred sand bass. Use for resting by bottom feeding diving birds, especially rafting surf scoter, scaup, and bufflehead (Bucephala albeola), and plunge divers, like terns and brown peli- cans, in moderately deep water is higher compared to other Bay locations (US Fish and Wildlife Service 1995a; Ogden 1995). Surf scoter and scaup have been declin- ing in San Diego Bay (Macdonald et al. 1990). The endangered California least tern and brown pelican forage in these areas. No information specific to this intermediate depth exists for invertebrates or plankton. Function Other than the fact that these areas have been left undisturbed by dredging for longer periods than deeper water, any ecological differences between deep and moderately deep habitats have not been quantified. State of the Bay—Ecosystem Resources 2-25 September 2000
  • 92. San Diego Bay Integrated Natural Resources Management Plan Photo © 1998 Tom Upton. Photo 2-3. Birds Rafting. 2.4.3 Shallow Subtidal Continually submerged, these shallow habitats extend from the low tide zone (–2.2 to –12 ft (2.2 to –12 ft/0.7 to –4 m MLLW). Shallow, soft bottom areas, with their associ- [–0.7 to –4 m] MLLW) ated fauna and flora, were the primary subtidal habitat in San Diego Bay prior to its development. About 3,734 acres (1,511 ha) (28%) presently dominate south „ About 3,734 acres (1,511 ha) Bay, portions of south-central Bay, and narrow strips along the shoreline of (28%) of shallow subtidal pres- north and north-central Bay. This represents an overall loss of 41% from historic ently dominate south Bay, por- proportions due to filling in of the Bay margins and dredging to deeper depths. tions of south-central Bay, and narrow strips along the shoreline South Bay has comparatively little disturbance from dredging, having last been of north and north-central Bay. dredged off NAB in 1941–1945. Exceptions are the Emory Cove channel, Chula This represents an overall loss of Vista Marina and the navigation channel leading to this marina. Sediment grain 41% from historic proportions. sizes tend to be very coarse (0 to 5% fines) to coarse (5 to 25% fines), except off the coast of NAB where fine sediments (up to 95% fines) accumulate. „ Waterbirds and fishes are more The abundance and biomass of fishes is much higher in shallow waters (Allen abundant in shallow waters close 1999). Bird abundance and diversity is also higher at these depths, possibly due to the shoreline. to the higher abundance of fish (Ogden 1994; US Fish and Wildlife Service 1995a). Shallow waters support many thousands of resident and migratory birds every year for foraging and resting. While all waterbirds are more abundant in shallow waters close to the shoreline, the groups that appear to use these areas preferentially are bottom feeding divers such as scoter and scaup, dabbling brant (Branta bernicla), plunge divers such as terns, and the surface-foraging black skimmer (Rynchops niger niger) (Ogden 1994; US Fish and Wildlife Service 1994a). 2.4.3.1 Unvegetated Habitat Description Shallow Soft Bottom Soft bottoms of unconsolidated sediment are unstable and shift in response to tides, wind, waves, currents, human activity, or biological activity such as feed- ing by bottom fishes, or bat rays (Myliobatis californica) excavating pits to reach buried clams. Few plants and animals have adapted to this instability—eelgrass is one of the few. Because animals and plants lack attachment sites in this envi- 2-26 State of the Bay—Ecosystem Resources September 2000
  • 93. San Diego Bay Integrated Natural Resources Management Plan ronment, they must burrow into the substrate to prevent from being washed away by currents, and so are called “infauna.” Competition for space is amelio- rated partly by organisms occupying various depths within the substrate. Inver- tebrates such as sponges, gastropod molluscs, and some larger crustaceans and tunicates live on the surface. Photo © 1999 San Diego Unified Port District. Photo 2-4. Ray on soft bottom sediment. „ Deposit feeding species tend to Different areas within this habitat have different species composition and abun- predominate in soft bottom sedi- dance, generally depending on time since last disturbance and composition of the ment areas, where they glean live substrate. Deposit feeding species, those that glean detritus once it has settled, tend and dead plankton. to predominate in soft bottom sediment areas with large amounts of silt and clay. The main reason for this relationship is that more detritus accumulates in the inter- stitial spaces among fine sediment particles than among those of larger grain size. In contrast, suspension feeders, those that filter material from the water column, are more common in areas where sandy sediments predominate, such as in portions of north Bay. „ Underwater observations indicate An important structural component of unvegetated shallows is the presence of that algal mats provide cover extensive masses or mats of living algal material interspersed with areas of exposed from predators for many species sediment that may extend into the intertidal zone (Ford 1968; Ford and Chambers of motile invertebrates and fishes, much like marsh vegetation does 1974). The dense, heavily branched red alga Gracilaria verrucosa forms the bulk for birds. of this mat, which also includes the red algae Hypnea valentiae and Griffithsia pacifica. Some of these plants are loosely anchored in the sediment, while oth- ers drift just above the bottom. Mats can be 1 to 2 ft (0.3 to 0.6 m) thick during the warmest months of the year. Underwater observations indicate that these algal mats are an important microhabitat feature, because they provide cover or ref- uge from predators for many species of motile invertebrates and fishes, much like marsh vegetation does for birds. The algae also appear to serve as a food source for some invertebrates. The living plant material and detritus constitute a primary food source for California killifish (Fundulus parvipinnis) and other fish, crabs, isopods, gastropod molluscs, and some aquatic birds (Macdonald et al. 1990). State of the Bay—Ecosystem Resources 2-27 September 2000
  • 94. San Diego Bay Integrated Natural Resources Management Plan Use of the Habitat „ Demersal fishes of unvegetated Unvegetated shallows support species assemblages of benthic invertebrates and shallow areas of soft sediment demersal fishes that are distinct from vegetated shallows (Kramer 1990; Takahashi feed on benthic invertebrates. 1992a; Allen 1997). Many of these invertebrates serve as food sources for the demer- sal fishes that are restricted to or occur primarily in these unvegetated shallow areas of soft sediment. An important example is the California halibut, a flatfish species of commercial and recreational value. The small juvenile halibut are restricted prima- rily to unvegetated shallows of unconsolidated sediment in bays and estuaries (Allen 1982; Kramer 1990), where they feed on invertebrate fauna (Drawbridge 1990). Unvegetated shallows therefore provide an important nursery for halibut. Other species of demersal fishes that appear to depend primarily on invertebrates of unvegetated shallows as their food source include the diamond turbot (Hyp- sopsetta guttulata), round stingray, and several species of gobies. In addition, many fishes that also occur in eelgrass and other vegetated shallow habitats feed both there and in unvegetated areas, as documented by the recent work of Allen (1998). Not surprisingly, studies in south Bay have shown that many of the fishes that occur in shallow subtidal habitats of south Bay also occur intertidally (Ford and Chambers 1973, 1974). Sediment characteristics at a given location are much the same both intertidally and subtidally. However, the number of intertidal species present generally appears to be much smaller than the number of subtidal species (Ford and Chambers 1973, 1974; Macdonald et al. 1990). Factors Affecting Composition and Stability of the Soft Bottom Community As in the deeper water environment, benthic organisms in shallow areas have very patchy distribution in space and time due to such variables as sediment composition, environmental disturbances, the nonrandom settlement and growth of larvae, pro- ductivity of the overlying water in terms of phytoplankton, life history strategies of organisms, competitive strategies, and predation by larger, active predators such as the round stingray and flatfishes. The stability of the soft bottom community depends upon the relative impor- tance of physical factors versus biological ones in structuring it. The major physi- cal and chemical factors that determine the structure of a soft bottom community and affect the population dynamics of its epifaunal and infaunal spe- cies involve a variety of characteristics of the sediment. They include grain size distribution, degree of grain compaction and porosity, water content, drainage (that is, whether it is stagnant or flushed at low tide), dissolved oxygen levels, lev- els of suspended and deposited organic material, and the short-term and long- term stability of the sediment. These characteristics are affected by depth, slope of the bottom, wave action, currents, and other physical and chemical characteris- tics of the water above the bottom. „ A stable, healthy community will Biological activity can also dominate community structure. For example, a relatively support larger infauna and a long-lived species, such as a sea cucumber, can dominate a shallow-water benthic greater diversity of infaunal life- community partly by modifying its physical environment through a series of stable styles. mounds and unstable intermediate areas to favor organisms compatible with itself. In that way, the sea cucumber-based community can remain stable for years. A sta- ble, healthy community will tend to support larger infauna (ghost shrimp, clams, etc.), and a diversity of infaunal life-styles such as suspension feeders, b