San Diego Bay National Wildlife Refuge

San Diego Bay National Wildlife Refuge Complex

6010 Hidden Valley Road

Carlsbad, CA 92011

Telephone: 760/930 0168

Fax: 760/930 0256

California Relay Service

TTY 1 800/735 2929

Voice 1 800/735 2922

U.S. Fish & Wildlife Service

http://pacific.fws.gov

For Refuge information

1 800/344 WILD

August 2006

Photo: USFWS/J. Konecny
Comprehensive Conservation Plans provide long-term guidance for management decisions 

and set forth goals, objectives, and strategies needed to accomplish refuge purposes and 

identify the Service’s best estimate of future needs. These plans detail program planning 

levels that are sometimes substantially above current budget allocations and, as such, are 

primarily for Service strategic planning and program prioritization purposes. The plans do 

not constitute a commitment for staffing increases, operational and maintenance increases, 

or funding for future land acquisition. 
San Diego Bay 

National Wildlife Refuge 

Sweetwater Marsh and South San Diego Bay Units

Final Comprehensive Conservation Plan and 

Environmental Impact Statement 

Volume II – August 2006 

Vision Statement 

The San Diego Bay National Wildlife Refuge protects a rich diversity of endangered, 

threatened, migratory, and native species and their habitats in the midst of a highly 

urbanized coastal environment. Nesting, foraging, and resting sites are managed for a 

diverse assembly of birds. Waterfowl and shorebirds over-winter or stop here to feed and 

rest as they migrate along the Pacific Flyway. Undisturbed expanses of cordgrassdominated salt marsh support sustainable populations of light-footed clapper rail. 

Enhanced and restored wetlands provide new, high quality habitat for fish, birds, and 

coastal salt marsh plants, such as the endangered salt marsh bird’s beak. Quiet nesting 

areas, buffered from adjacent urbanization, ensure the reproductive success of the 

threatened western snowy plover, endangered California least tern, and an array of 

ground nesting seabirds and shorebirds. 

The San Diego Bay National Wildlife Refuge also provides the public with the opportunity 

to observe birds and wildlife in their native habitats and to enjoy and connect with the 

natural environment. Informative environmental education and interpretation programs 

expand the public’s awareness of the richness of the wildlife resources of the Refuge. The 

Refuge serves as a haven for wildlife and the public to be treasured by this and future 

generations. 

U. S. Fish and Wildlife Service 

California/Nevada Refuge Planning Office 

2800 Cottage Way, Room W-1832 

Sacramento, CA 95825 

August 2006

U.S. Fish & Wildlife Service
Appendices (Volumes II and III) 

Appendix A. Glossary of Terms 

Appendix B. Distribution Lists

Appendix C. Bird Species Lists 

Appendix D. CCP Implementation 

Appendix E. Summary of Public Scoping Comments 

Appendix F. Description of the Salt Works Operation 

Appendix G. Federal and State Ambient Air Quality Standards 

Appendix H. Air Quality Calculations 

Appendix I. Hydrodynamic Modeling Analysis

Appendix J. Desalinization and Brine Management Feasibility Assessment

Brine Modeling 

Appendix K. Compatibility Determinations 

Appendix L. Fire Management Plan for the San Diego NWR Complex 

Appendix M. Predator Management Plan 

Appendix N. Wilderness Inventory 

Appendix O. Letter from the California Department of Fish and Game 

Appendix P. Responses to Comments (Volume III)
 

Appendix A 

 Glossary of Terms
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement A-1 

Appendix A: Glossary of Terms

1. Acronyms and Abbreviations

AAR Acquisition Ascertainment Report 

ACHP Advisory Council on Historic Preservation 

ACOE United States Army Corps of Engineers 

ADA Americans with Disabilities Act 

ADT average daily traffic volumes 

AHPA Archaeological and Historic Preservation Act 

Airport Authority San Diego County Regional Airport Authority 

APCD San Diego Air Pollution Control District 

APE Area of Potential Effect 

ARB California Air Resources Board 

ARPA Archaeological Resources Protection Act 

BCR Bird Conservation Regions 

BMPs Best Management Practices 

BOD biological oxygen demand 

Caltrans California Department of Transportation 

CAP Contaminant Assessment Process 

CAAQS California Ambient Air Quality Standards 

CCP Comprehensive Conservation Plan 

CDFG California Department of Fish and Game 

CEQA California Environmental Quality Act 

CESA California Endangered Species Act 

CFR Code of Federal Regulations 

cfs cubic feet per second 

cm centimeter 

CNEL Community Noise Equivalent Level 

CO Carbon monoxide 

Code California Fish and Game Code 

combined federal project Sweetwater River Flood Control Channel/State Highway Route 

54/Interstate 5 Project 

Commission California State Historic Resources Commission 

Complex San Diego National Wildlife Refuge Complex 

County County of San Diego 

CRMP Cultural Resources Management Program 

dB decibel 

dBA A-weighted” noise scale 

dB Leq noise levels presented as average noise levels over a period of 

minutes or hours 

DDT Dichlorodiphenyltrichloroethane 

DEA Draft environmental sssessment 

DEIS Draft Environmental Impact Statement 

DOI Department of the Interior 

DU Ducks Unlimited 
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A-2 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

EA environmental assessment 

EBS Environmental Business Solutions, Inc. 

EIS Environmental Impact Statement 

EPA U.S. Environmental Protection Agency 

ESA Federal Endangered Species Act 

FEMA Federal Emergency Management Agency 

FR Federal Register 

FTE full-time equivalent 

FY Fiscal Year 

gpm gallons per minute 

HMP Habitat Management Plan 

HRB Historical Resources Board (City of San Diego) 

HUD U.S. Department of Housing and Urban Development 

I-5 Interstate 5 

Improvement Act National Wildlife Refuge System Improvement Act of 1997 

INRMP San Diego Bay Integrated Natural Resources Management Plan 

kV kilovolt 

LCP Local Coastal Program 

LEA County of San Diego Department of Environmental Health, Solid 

Waste Local Enforcement Agency 

Ldn Day/Night Average Sound Level 

LOS Level of Service 

LPP Land Protection Plan 

m2 square meter 

μg/m3 micrograms per cubic meter 

MBTA Migratory Bird Treaty Act 

MHHW mean higher high water 

MHPA Multi-Habitat Planning Area, as defined in the City of San Diego’s 

Multiple Species Conservation Program Subarea Plan 

MHW mean high water 

MLLW mean low low water 

MOA memorandum of agreement 

MOU Memorandum of Understanding 

MPAs Marine Protected Areas 

mph miles per hour 

MSCP Multiple Species Conservation Program 

MSL Mean Sea Level 

MTDB Metropolitan Transit Development Board 

Municipal Permit Municipal Storm Water NPDES Permit 

NAAQS National Ambient Air Quality Standards 

NAGPRA Native American Graves Protection and Repatriation Act 

NASNI Naval Air Station, North Island 

NGOs non-government organizations 

NEPA National Environmental Policy Act 

NGDV National Geodetic Vertical Datum 

NHPA National Historic Preservation Act 

NMFS National Marine Fisheries Service 

NO2 Nitrogen dioxide 

NOAA National Oceanic and Atmospheric Administration 

NOI Notice of Intent 

NOLF Navel Outlying Landing Field, Imperial Beach 
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NOx Oxides of nitrogen 

NPDES National Pollutant Discharge Elimination System 

NRHP National Register of Historic Places 

NRRF Naval Radio Receiving Facility 

NWI National Wetlands Inventory 

NWR National Wildlife Refuge 

NWRS National Wildlife Refuge System 

O3 Ozone 

OEHHA Office of Environmental Health Hazard Assessment 

OVRP Otay Valley Regional Park 

PAHs polycyclic aromatic hydrocarbons 

PCBs polychlorinated biphenyls 

PM10 fugitive dust emissions or “inhalable particles” that are 10 microns 

(millionths of a meter) or less in diameter 

PM2..5 fine inhalable particles that are 2.5 microns and smaller 

Port Unified Port of San Diego (formerly San Diego Unified Port 

District, SDUPD) 

ppm parts per million 

ppt parts per thousand 

PRISM Program for Regional and International Shorebird Monitoring 

PWC personal watercraft 

ROD Record of Decision 

RONS Refuge Operating Needs System 

RWQCB Regional Water Quality Control Board 

SANDAG San Diego Association of Governments 

SDUPD or Port San Diego Unified Port District, now referred to 

as the Unified Port of San Diego 

Service U.S. Fish and Wildlife Service (also, USFWS) 

SHPO State Historic Preservation Office 

SO4 Sulfates 

SOHO Save Our Heritage Organization 

SR 56 State Route 56 

SSA Special Study Area 

State California Department of Fish and Game 

SUP Special Use Permit 

SWIA Southwest Wetlands Interpretive Association 

SWRCB California State Water Resources Control Board 

TACAN instrument approach for NASNI 

TBT tributyltin 

TEA-21 Transportation Enhancement Act for the 21st Century 

THPO Tribal Historic Preservation Officer 

TOT transit occupancy taxes 

TRPH total recoverable petroleum hydrocarbons 

USC United States Code 

USDA U.S. Department of Agriculture 

USDA APHIS U.S. Department of Agriculture, Animal Plant Health Inspection 

Service 

USFWS U.S. Department of the Interior, Fish and Wildlife Service (also, 

Service) 

VFR visual flight rules 

VOC volatile organic compounds 
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A-4 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

2. Glossary of Terms 

Abiotic. The non-living parts of an ecosystem (e.g. light, temperature, water, oxygen, and other 

nutrients or gases). 

Accessibility. The state or quality of being easily approached or entered, particularly as it relates 

to complying with the Americans With Disabilities Act. 

Accumulation. The build-up of a chemical in an organism due to repeated exposure. 

Adaptive Management. The rigorous application of management, research, and monitoring to 

gain information and experience necessary to assess and modify management activities. A process 

that uses feedback from refuge research and monitoring and evaluation of management actions to 

support or modify objectives and strategies at all planning levels. Analysis of results help 

managers determine whether current management should continue as is or whether it should be 

modified to achieve desired conditions. 

Alluvial. Clay, silt, sand, gravel or other sedimentary matter transported and deposited in a delta 

or riverbed by flowing water. 

Alternative. A reasonable way to fix an identified problem or satisfy a stated need, or a different 

set of objectives and strategies or means of achieving refuge purposes and goals, helping fulfill the 

refuge system mission, and resolving issues. 

Approved Acquisition Boundary. A project boundary that the Director of the Service approves 

upon completion of the planning and environmental compliance process. An approved acquisition 

boundary only designates those lands which the Service has authority to acquire or manage 

through various agreements. The approval of an acquisition boundary does not grant the Service 

jurisdiction or control over lands within the boundary, and it does not make lands within the refuge 

boundary part of the National Wildlife Refuge System. Lands do not become part of the System 

until the Service buys them or they are placed under an agreement that provides for their 

management as part of the System. 

Aquatic. Pertaining to water, in contrast to land. 

Artifact. An object used or made by humans, usually in reference to projectile points, tools, 

utensils, art, food remains, and other products of human activity. 

Benthic. Refers to organisms associated with the bottom of the ocean, bay, lake, or river. 

Biodiversity (Biological Diversity). Refers to the full range of variability within and among 

biological communities, including genetic diversity, and the variety of living organisms, 

assemblages of living organisms, and biological processes. Diversity can be measured in terms of 

the number of different items (species, communities) and their relative abundance. 

Biological Integrity. Biotic composition, structure, and functioning at the genetic, organism, and 

community levels consistent with natural conditions, including the natural biological processes that 

shape genomes, organisms, and communities. 

Biota. The plant and animal life of a region. 
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Bivalve. Common term for pelecypods (members of Mollusca) in which the hard parts are 

composed of two sections fitting together to enclose a space that contains the soft part of the 

organism. 

Categorical Exclusion. A category of actions that do not individually or cumulatively have a 

significant effect on the human environment and have been found to have no such effect in 

procedures adopted by a Federal agency pursuant to the National Environmental Policy Act. 

Compatibility Determination. A written determination that a proposed or existing use of a 

National Wildlife Refuge is a compatible use or is not a compatible use. 

Compatible Use. A proposed or existing wildlife-dependent recreational use or any other use of a 

National Wildlife Refuge that, based on sound professional judgment, will not materially interfere 

with or detract from the fulfillment of the National Wildlife Refuge System Mission or the 

purposes of the Refuge on which the use would occur. 

 

Comprehensive Conservation Plan (CCP). A document that describes the desired future 

conditions of the refuge or planning unit and provides long-range guidance and management 

direction to achieve the purposes of the refuge, helps fulfill the mission of the Refuge System; 

maintains and, where appropriate, restores the ecological integrity of each refuge and the Refuge 

System; helps achieve the goals of the National Wilderness Preservation System; and meets other 

mandates. 

Concern. See issue. 

Critical Habitat. According to U.S. Federal law, the ecosystems upon which endangered and 

threatened species depend. 

Cultural Resource. The physical remains of human activity (artifacts, ruins, petroglyphs, etc.) 

and conceptual content or context of an area such as a traditional sacred site. It includes 

historically, archaeologically and architecturally significant resources. 

Cultural Resource Inventory. A professionally conducted study designed to locate and evaluate 

evidence of cultural resources present within a defined geographic area. Inventories may involve 

various levels, including background literature search, comprehensive field examination to identify 

all exposed physical manifestations of cultural resources, or sample inventory to project site 

distribution and density over a larger area. Evaluation of identified cultural resources to determine 

eligibility for the National Register follows the criteria found in 36 CFR 60.4. 

Cultural Resource Overview. A comprehensive document prepared for a field office that 

discusses, among other things, its prehistory and cultural history, the nature and extent of known 

cultural resources, previous research, management objectives, resource management conflicts or 

issues, and a general statement on how program objectives should be met and conflicts resolved. 

Detritus. An accumulation of decomposing plant and animal remains. 

Dioxin. A family of toxic chemicals, including polychlorinated biphenyls (PCBs), that all share a 

similar chemical structure and a common mechanism of toxic action. Dioxin levels in the 

environment have been declining; however, current exposures levels still remain a concern. 
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A-6 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Disturbance. Significant alteration of habitat structure or composition. May be natural (e.g., fire) 

or human-caused events (e.g., aircraft overflight). Also see wildlife disturbance. 

Easement. A privilege or right that is held by one person or other entity in land owned by 

another. 

Ecological Integrity. The integration of biological integrity, natural biological diversity, and 

environmental health; the replication of natural conditions. 

Ecoregion. A territory defined by a combination of biological, social, and geographic criteria, 

rather than geopolitical considerations; generally, a system of related, interconnected ecosystems. 

Ecosystem. A dynamic and interrelating complex of plant and animal communities and their 

associated non-living environment. 

Ecosystem Approach. Protecting or restoring the natural function (processes), structure 

(physical and biological patterns), and species composition of an ecosystem, recognizing that all 

components are interrelated. 

Ecosystem Management. Management of natural resources using system-wide concepts to 

ensure that all plants and animals in ecosystems are maintained at viable levels in native habitats 

and basic ecosystem processes are perpetuated indefinitely. 

Effect. A change in a resource, caused by a variety of events including project attributes acting on 

a resource attribute (direct), not directly acting on a resource attribute (indirect), another project 

attributes acting on a resource attribute (cumulative), and those caused by natural events (e.g., 

seasonal change). 

Endangered Species (Federal). A plant or animal species listed under the Endangered Species 

Act that is in danger of extinction throughout all or a significant portion of its range. 

Endangered Species (State). A plant or animal species in danger of becoming extinct or 

extirpated in California within the near future if factors contributing to its decline continue. 

Environment. The sum total of all biological, chemical, and physical factors to which organisms 

are exposed; the surroundings of a plant or animal. 

Environmental Assessment (EA). A concise public document, prepared in compliance with the 

National Environmental Policy Act, that briefly discusses the purpose and need for an action, 

alternatives to such action, and provides sufficient evidence and analysis of impacts to determine 

whether to prepare an Environmental Impact Statement or Finding of No Significant Impact. 

Environmental Education. A process designed to develop a citizenry that has the awareness, 

concern, knowledge, attitudes, skills, motivation, and commitment to work toward solutions of 

current environmental problems and the prevention of new ones. Environmental education within 

the National Wildlife Refuge System incorporates materials, activities, programs, and products 

that address the citizen's course of study goals, the objectives of the refuge or unit, and the mission 

of the Refuge System. 
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Environmental Health. Abiotic composition, structure, and functioning of the environment 

consistent with natural conditions, including the natural abiotic processes that shape the 

environment. 

Environmental Impact Statement (EIS). A detailed written statement required by Section 

102(2)(C) of the National Environmental Policy Act, analyzing the environmental impacts of a 

proposed action, adverse effects of the project that cannot be avoided, alternative courses of action, 

short-term uses of the environment versus the maintenance and enhancement of long-term 

productivity, and any irreversible and irretrievable commitment of resources (40 CFR 1508.11). 

Epibenthic. Pertaining to the environment and conditions of organisms living near the water 

bottom. 

Estuarine. Deepwater tidal habitats and adjacent tidal wetlands that are usually partly enclosed 

by land but have some access to the open ocean and are diluted by freshwater. 

Estuary. The wide lower course of a river into which the tides flow. The area where the tide 

meets a river current. 

Euryhaline. Organisms that are tolerant of a wide range of salinity. 

Exotic Species. Species that have been intentionally introduced to or have inadvertently 

infiltrated an area in which they are not natural found. Exotic species compete with native species 

for food or habitat. 

Fallow. Allowing land that normally is used for crop production to lie idle. 

Federal Trust Resources. A trust is something managed by one entity for another who holds the 

ownership. The Service holds in trust many natural resources for the people of the United States of 

America as a result of Federal acts and treaties. Examples are species listed under the 

Endangered Species Act, migratory birds protected by the Migratory Bird Treaty Act and other 

international treaties, and native plant or wildlife species found on the Refuge System. 

Finding of No Significant Impact (FONSI). A document prepared in compliance with the 

National Environmental Policy Act, supported by an environmental assessment, that briefly 

presents why a Federal action will have no significant effect on the human environment and for 

which an environmental impact statement, therefore, will not be prepared (40 CFR 1508.13). 

Floodplain. The relatively flat area along the sides of a river which is naturally subjected to 

flooding. 

Fluvial. Pertaining to a river. 

Flyway. A route taken by migratory birds between their breeding grounds and their wintering 

grounds. Four primary migration routes have been identified for birds breeding in North 

America: the Pacific, Central, Mississippi, and Atlantic Flyways. 

Foraging. The act of feeding; another word for feeding. 

Forb. A broad-leaved, herbaceous plant. 
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A-8 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Fragmentation. The process of reducing the size and connectivity of habitat patches. 

Gastropod. Any of a large class of mollusks, usually with a univalve shell or no shell and a distinct 

head bearing sensory organs, such as snails and slugs. 

Goal. Descriptive, open-ended, and often broad statement of desired future conditions that 

conveys a purpose but does not define measurable units. 

Habitat. Suite of existing environmental conditions required by an organism for survival and 

reproduction. The place where an organism typically lives. 

Habitat Fragmentation. The breaking up of a specific habitat into smaller, unconnected areas. 

Habitat Restoration. Management emphasis designed to move ecosystems to desired conditions 

and processes, and/or to healthy ecosystems. 

Habitat Type. See Vegetation Type. 

Hydrologic Regime. The local pattern and magnitude of water flow influenced by season. 

Hydrology. The science dealing with the properties, distribution, and circulation of water on and 

below the earth's surface and in the atmosphere. The distribution and cycling of water in an area. 

Impact. Refer to Effect. 

Integrated Pest Management (IPM). Methods of managing undesirable species, such as weeds, 

including education; prevention, physical or mechanical methods or control; biological control; 

responsible chemical use; and cultural methods. 

Interpretation. Interpretation can be an educational and recreational activity that is aimed at 

revealing relationships, examining systems, and exploring how the natural world and human 

activities are interconnected. 

Intertidal Mudflat. Expanses of mud contiguous to a water body often covered and exposed by 

tides. 

Invasive Species. Refer to Exotic Species. 

Inversion. A state in which the temperature of the air increases with increasing altitude and keeps 

the surface air and pollutants down. 

Invertebrate. Animals that do not have backbones. Included are insects, spiders, mollusks (clams, 

snails, etc.), and crustaceans (shrimp, crayfish, etc.). 

Issue. Any unsettled matter that requires a management decision (e.g., a Service initiative, 

opportunity, resource management problem, a threat to the resources of the unit, conflict in uses, 

public concern, or the presence of an undesirable resource condition). 
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Landbird. A category of birds that obtains at least part of their food from the land and nest in 

mainland areas (though some can also be found on islands). Landbirds include raptors and 

songbirds among others. 

Landform. The physical shape of the land reflecting geologic structure and processes of 

geomorphology that have sculpted the structure. 

Landowner: A person or entity indicated as the owner of property on the various ownership maps 

maintained by the Office of the County Assessor. 

Lease. A legal contract by which rights to use land or water are acquired for a specified period of 

time for a specified rent or compensation. 

Levee. An embankment along the river or other body of water that retains water within the water 

body. 

Macroinvertebrates. Invertebrates large enough to be seen with the naked eye (e.g., most aquatic 

insects, snails, and amphipods). 

Management Alternative. A set of objectives and the strategies needed to accomplish each 

objective [FWS Manual 602 FW 1.4]. 

Management Concern. Refer to Issue. 

Marsh. A periodically wet or continually flooded area where the water is shallow enough to allow 

the growth of emergent vegetation; a marsh can be influenced by freshwater, tides, or both. 

Marsh Habitat. Habitat that is characterized by shallow water and emergent vegetation; unless 

otherwise specified, this term does not apply to similar habitat found in rivers, drains, or canals. 

Migration. The seasonal movement from one area to another and back. 

Migratory Bird. A bird that seasonally moves between geographic areas. 

Mitigation. To avoid or minimize impacts of an action by limiting the degree or magnitude of the 

action; to rectify the impact by repairing, rehabilitating, or restoring the affected environment; to 

reduce or eliminate the impact by preservation and maintenance operations during the life of the 

action. 

Model. A mathematical formula that expresses the actions and interactions of the elements of a 

system in such a manner that the system may be evaluated under any given set of conditions. 

Monitoring. The process of collecting information to track changes of selected parameters over 

time. Monitoring is necessary to identify, track and analyze results of management actions at the 

Refuge so that future management actions may be adapted to obtain the best benefits to wildlife 

and habitat. See also Adaptive Management. 

National Environmental Policy Act (NEPA). An act which encourages productive and 

enjoyable harmony between humans and their environment, to promote efforts that will prevent or 

eliminate damage to the environment and atmosphere, to stimulate the health and welfare of 
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A-10 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

humans. The act also established the Council on Environmental Quality. The Act requires all 

agencies, including the Service, to examine the environmental impacts of their actions, incorporate 

environmental information, and use public participation in the planning and implementation of all 

actions. Federal agencies must integrate NEPA with other planning requirements, and prepare 

appropriate NEPA documents to facilitate better environmental decision making. 

National Wildlife Refuge (Refuge or NWR). A designated area of land or water or an interest in 

land or water within the Refuge System, including National Wildlife Refuges, Wildlife Ranges, 

Wildlife Management Areas, Waterfowl Production Areas, and other areas (except Coordination 

Areas) under Service jurisdiction for the protection and conservation of fish and wildlife. 

National Wildlife Refuge System. Various categories of areas administered by the Secretary of 

the Interior for the conservation of fish and wildlife, including species threatened with extinction; 

all lands, waters, and interests therein administered by the Secretary as wildlife refuges; areas for 

the protection and conservation of fish and wildlife that are threatened with extinction; wildlife 

ranges; games ranges; wildlife management areas; or waterfowl production areas. 

National Wildlife Refuge System Improvement Act of 1997 (Public Law 105-57). Under the 

Refuge Improvement Act, the Service is required to develop 15-year Comprehensive Conservation 

Plans for all National Wildlife Refuges outside Alaska. The Act also describes the six public uses 

given priority status within the NWRS (i.e., hunting, fishing, wildlife observation, photography, 

environmental education, and interpretation). 

National Wildlife Refuge System Mission. "The mission of the system is to administer a 

National network of lands and waters for the conservation, management, and, where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United States for 

the benefit of present and future generations of Americans." 

Native Species. Species that normally live and thrive in a particular ecosystem. 

Natural Recruitment. Plant establishment through natural processes. 

Neotropical Migratory Birds. Migratory birds that breed in North American and winter in 

Central and South America. 

No Action Alternative. An alternative under which existing management would be continued. 

Notice of Intent (NOI). A notice that is published in the Federal Register announcing that an 

Environmental Impact Statement will be prepared and considered for a specific action. 

Objective. An objective is a concise target statement of what will be achieved, how much will be 

achieved, when and where it will be achieved, and who is responsible for the work. Objectives are 

derived from goals and provide the basis for determining management strategies. Objectives 

should be attainable and time-specific and should be stated quantitatively to the extent possible. If 

objectives cannot be stated quantitatively, they may be stated qualitatively. 

One-Hundred-Year Floodplain. The relatively flat portion of the river channel that has a one 

percent chance of being inundated by flood water in any given year. 

Opportunities. Potential solutions to issues. 
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Ordinary High Water Mark. That line on the shore established by the fluctuations of water and 

indicated by physical characteristics such as clear, natural line impressed on the bank, shelving, 

changes in the character of soil, destruction of terrestrial vegetation, the presence of litter and 

debris, or other appropriate means that consider the characteristics of the surrounding areas. 

Outreach. Two-way communication between the Service and the public to establish mutual 

understanding, promote involvement, and influence attitudes and actions, with goal of improving 

joint stewardship of our natural resources. 

Overbank Flooding. River flows that exceed the boundaries of the existing river channel and/or 

levees and flood adjacent areas. 

Passerine Bird. A songbird or other perching bird that is in the order Passeriformes (blackbirds, 

crows, warblers, sparrows, and wrens for example). 

Peak Flow. The maximum discharge of a stream or river during a specified period of time. 

Perennial. In reference to a body of water, one that contains water year-to-year and that rarely 

goes dry. 

Permeability. The property or capacity of porous rock, sediment, or soil to transmit water. 

Personal Watercraft. Personal watercraft (PWC) are small vessels that use inboard motors to 

power water jet pumps. They are known by such trade names as Jet-ski, Waverunner, and SeaDoo. Personal watercraft are high performance vessels, designed for speed. 

Phenology. The life cycle of particular species. 

Planning Area. The area upon which a planning effort is focused. 

Planning Team. A team or group of persons working together to prepare a document. Planning 

teams are interdisciplinary in membership and function and generally consist of a planning team 

leader, refuge manager and staff biologists, a state natural resource agency representative, and 

other appropriate program specialists (e.g., social scientist, ecologist, recreation specialist). 

Planning Unit or Unit. A single refuge, an ecologically or administratively related refuge 

complex, or distinct unit of a refuge. The planning unit also may include lands currently outside 

refuge boundaries. 

Plant Association. A classification of plant communities based on the similarity in dominants of 

all layers of vascular species in a climax community. 

Plant Community. An assemblage of plant species of a particular composition. The term can also 

be used in reference to a group of one or more populations of plants in a particular area at a 

particular point in time; the plant community of an area can change over time due to disturbance 

(e.g., fire) and succession. 

Pollutant or Contaminant. Any introduced gas, liquid, or solid that makes a resource unfit for a 

specific purpose. 
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A-12 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Polychaetes. Any of a class (Polychaeta) of chiefly marine annelid worms (such as clam worms), 

usually with paired segmental appendages, separate sexes, and a free-swimming trochophore 

larva. 

Polychlorinated Biphenyls (PCBs). A mixture of individual chemicals which are no longer 

produced in the United States, but are still found in the environment. 

Polycyclic Aromatic Hydrocarbons (PAHs). A group of over 100 different chemicals that are 

formed during the incomplete burning of coal, oil and gas, garbage, or other organic substances 

like tobacco or charbroiled meat. PAHs are usually found as a mixture containing two or more of 

these compounds, such as soot. 

Population. All the members of a single species coexisting in one ecosystem at a given time. 

Preferred Alternative. This is the alternative determined by the decision maker to best achieve 

the Refuge purpose, vision, and goals; contributes to the Refuge System mission, addresses the 

significant issues; and is consistent with principles of sound fish and wildlife management. 

Prescribed Fire. The skillful application of fire to natural fuels under conditions of weather, fuel 

moisture, soil moisture, etc., that allows confinement of the fire to a predetermined area and 

produces the intensity of heat and rate of spread to accomplish planned benefits to one or more 

objectives of habitat management, wildlife management, or hazard reduction. 

Prime Farmland. Farmland in an area or region that is considered to be the most ideal farmland 

based on several criteria; usually soil types and land productivity of the land are two of the most 

important criteria. 

Priority Public Uses. Compatible wildlife-dependent recreation uses (hunting, fishing, wildlife 

observation and photography, and environmental education and interpretation). 

Proposed Action. The Service’s proposed action for Comprehensive conservation Plans. 

Public. Individuals, organizations, and groups; officials of Federal, State, and local government 

agencies; Indian tribes; and foreign nations. It may include anyone outside the core planning team. 

It includes those who may or may not have indicated an interest in Service issues and those who do 

or do not realize that Service decisions may affect them. 

Public Involvement. A process that offers impacted and interested individuals and organizations 

an opportunity to become informed about, and to express their opinions on Service actions and 

policies. In the process, these views are studied thoroughly and thoughtful consideration of public 

views is given in shaping decisions for refuge management. 

Public Scoping: See Public Involvement. 

Purpose(s) of the Refuge. The purpose of a refuge is specified in or derived from the law, 

proclamation, executive order, agreement, public land order, donation document, or administrative 

memorandum establishing, authorization, or expanding a refuge, refuge unit, or refuge subunit. 

Raptor. A category of carnivorous birds, most of which have heavy, sharp beaks, strong talons, 

and take live prey (e.g., peregrine falcon, northern harrier). Also referred to as a bird of prey. 
Appendix A ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement A-13

Record of Decision (ROD). A concise public record of decision prepared by the Federal agency, 

pursuant to NEPA, that contains a statement of the decision, identification of all alternatives 

considered, identification of the environmentally preferable alternative, a statement as to whether 

all practical means to avoid or minimize environmental harm from the alternative selected have 

been adopted (and if not, why they were not), and a summary of monitoring and enforcement 

where applicable for any mitigation. 

Recruitment. The annual increase in a population as determined by the proportion of surviving 

offspring produced during a specific period (usually expressed per year). 

Refuge Goal. Refer to Goal. 

Refuge Operating Needs System (RONS). A national database that contains the unfunded 

operational needs of each refuge. The Service includes projects required to implement approved 

plans and meet goals, objectives, and legal mandates. 

Refuge Purposes. Refer to Purposes of a Refuge. 

Refuge Revenue Sharing Program. Provides payments to counties in lieu of taxes using 

revenues derived from the sale of products from refuges. 

Refuge Use. Any activity on a refuge, except administrative or law enforcement activity carried 

out by or under the direction of an authorized service employee. 

Refuge Vision. A succinct statement of the unit's purpose and reason for being. 

Restoration. The return of an ecosystem to an approximation of its former unimpaired condition. 

Revetment. A facing of stone, concrete, or other material placed on a riverbank to protect it from 

erosion. 

Rhizomes. Rootlike stem growing horizontally below the surface. The rhizome is used for food 

storage and can produce roots and shoots. 

Riparian. Refers to an area or habitat that is transitional from terrestrial to aquatic ecosystems; 

including streams, lakes wet areas, and adjacent plant communities and their associated soils 

which have free water at or near the surface; an area whose components are directly or indirectly 

attributed to the influence of water; of or relating to a river; specifically applied to ecology, 

“riparian” describes the land immediately adjoining and directly influenced by streams. For 

example, riparian vegetation includes any and all plant life growing on the land adjoining a stream 

and directly influenced by the stream. 

Riparian Area. A transitional between terrestrial and aquatic ecosystems, distinguished by 

gradients in biophysical conditions, ecological processes, and biota; areas through which surface 

and subsurface hydrology connect waterbodies with their adjacent uplands. 

Riparian Habitat. Gravel bars, sand dunes, non-vegetated riverbanks, herbaceous, scrub and 

forested vegetation, which provides habitat for plants, macro-invertebrates, fish and wildlife. 
Appendix A ──────────────────────────────────────────────

A-14 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Riverine. Freshwater wetlands and deepwater habitats within a channel containing periodically or 

continuously moving water. It includes wetlands with primarily or mostly submerged vegetation 

but does not include those wetlands with mostly emergent vegetation or shrubs and trees. This 

habitat encompasses a river or stream, its channel, and the associated aquatic vegetation. Can also 

pertain to rivers and floodplains. 

Seabird. A group of birds that obtain at least some food from the ocean by traveling some distance 

over its surface. They also typically breed on islands and along coastal areas. Seabirds include 

gulls, terns, pelicans, and cormorants, among others. 

Sediment. Any material, carried in suspension by water, which ultimately settles to the bottom of 

water courses. Sediments may also settle on stream banks or flood plains during high water flow. 

Shorebirds. Long-legged birds, also known as waders, belonging to the order Charadriiformes, 

which use shallow wetlands and mud flats for foraging and nesting. 

Soil Erosion. The wearing away of the land's surface by water, wind, ice, or other physical 

process. 

Songbirds. A category of birds that are medium to small, perching landbirds. Most are territorial 

singers and migratory. (Refer also to Passerines.) 

Sound Professional Judgment. A finding, determination, or decision that is consistent with 

principles of sound fish and wildlife management and administration, available science and 

resources, and adherence to the requirements of the Refuge Administration Act of 1966 (16 U.S.C. 

668dd-668ee), and other applicable laws. Included in the finding, determination, or decision is a 

refuge manager’s field experience and knowledge of the particular refuge’s resources. 

Species. A distinctive kind of plant or animal having distinguishable characteristics, and that can 

interbreed and produce young. A category of biological classification. 

Species Composition. A group of species that inhabit a specific habitat type in its healthy state. 

Species Diversity. Usually synonymous with “species richness,” but may also include the 

proportional distribution of species. 

Step-down Management Plan. A plan that provides specific guidance on management subjects 

(e.g., habitat, public use, fire, safety) or groups of related subjects. It describes strategies and 

implementation schedules for meeting CCP goals and objectives. 

Strategy. A specific action, tool, or technique or combination of actions, tools, and techniques used 

to meet unit objectives. 

Study Area. The area reviewed in detail for wildlife, habitat, and public use potential. For 

purposes of this CCP/EIS the study area includes the land and water within the approved Refuge 

boundary. 

Sublittoral. Relating to or describing an organism living immediately below low-tide level. 

Submergent Vegetation. Plants that grows completely submerged except when flowering. 
Appendix A ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement A-15

Subsidence. Movement to a lower level or elevation. 

Surface Water. A body of water that has its upper surface exposed to the atmosphere. 

Terminus. In reference to a stream or river, its end point; where it flows into a lake or other 

basin. 

Threatened Species (Federal). Species listed under the Endangered Species Act that are likely 

to become endangered within the foreseeable future throughout all or a significant portion of their 

range. 

Tiering. The coverage of general matters in broader environmental impact statements with 

subsequent narrower statements of environmental analysis, incorporating by reference, the 

general discussions and concentrating on specific issues. 

Trace Elements. Metallic elements generally occurring in trace amounts in water, including iron, 

manganese, copper, chromium, arsenic, mercury, and vanadium. 

Turbidity. Cloudiness of a water body caused by suspended silt, mud, pollutants, or algae. 

U.S. Fish and Wildlife Service Mission. “Working with others to conserve, protect, and enhance 

fish, wildlife, and plants and their habitats for the continuing benefit of the American people. 

Understory. Shrubs and herbaceous plants that typically grow beneath larger trees or shrubs. 

Upland. An area where water normally does not collect and where water does not flow on an 

extended basis. Uplands are non-wetland areas. 

Vegetation. The composition of plant species, their frequency of occurrence, density, and age 

classes at a specified scale. 

Vegetation Community. Refer to Plant Community. 

Vegetation Type or Habitat Type. A land classification system based upon the concept of distinct 

plant associations. 

Waterfowl. A group of birds that include ducks, geese, and swans (belonging to the order 

Anseriformes). 

Watershed. The entire land area that collects and drains water into a river or river system. 

Wetland. Land that is transitional between upland (terrestrial) and aquatic systems (greater than 

about 6-feet deep) where the water table is usually at or near the surface or the land is covered by 

shallow water. 

Wetland Habitat. Habitat provided by shallow or deep water (but less than 6-feet deep), with or 

without emergent and aquatic vegetation in wetlands. Wetland habitat only exists when and where 

a wetland or portion of a wetland is covered with water (visible surface water). Consequently, the 

size and shape of "wetland habitat" will fluctuate from season to season and year to ear while the 
Appendix A ──────────────────────────────────────────────

A-16 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

size and shape of the "wetland" within which wetland habitat occurs will remain constant from 

season to season and from year to year. 

Wildfire or Wildland Fire. A free-burning fire requiring a suppression response; all fire other 

than prescribed fire that occurs on wildlands. 

Wildlife. All non-domesticated animal life; included are vertebrates and invertebrates.

Wildlife Corridor. A landscape feature that facilitates the biologically effective transport of 

animals between larger patches of habitat dedicated to conservation functions. Such corridors may 

facilitate several kinds of traffic, including frequent foraging movement, seasonal migration, or the 

once in a lifetime dispersal of juvenile animals. These are transition habitats and need not contain 

all the habitat elements required for long-term survival of reproduction of its migrants. 

Wildlife-Dependent Recreational Use. "A use of a refuge involving hunting, fishing, wildlife 

observation and photography, or environmental education and interpretation." These are the six 

priority public uses of the Refuge System as established in the National Wildlife Refuge System 

Administration Act, as amended. 
 

Appendix B 

 Distribution List
────────────── Final Comprehensive Conservation Plan/Environmental Impact Statement B-1

Appendix B: Distribution Lists

1. Distribution List for the Draft Comprehensive Conservation 

Plan/Environmental Impact Statement

The following individuals, organizations, local businesses, Tribal governments, 

interested media, public agencies, and elected officials received notice of the 

availability of the San Diego Bay National Wildlife Refuge (Sweetwater Marsh and 

South San Diego Bay Units) Draft Comprehensive Conservation 

Plan/Environmental Impact Statement (CCP/EIS). 

Individuals

Acheatel, David 

Adams, Duane 

Adams, Lissa 

Adler, Gerrold 

Aguila, Gabriela 

Aguilar, Maricela 

Aguirre, Barbara 

Alfaro, Monica 

Allds, Richard 

Almanza, Lindsay 

Amador, Luz 

Anderson, Barbara 

Anderson, John 

Ansley, Wayne 

Armour, Mike 

Arzola, Raul 

Ayala, Leticia 

Backal, Jack 

Baclagan, Cynthia 

Baird, Terry 

Ball, Alan 

Ballis, Douglas 

Barienbrock, Gordon 

Barlow, Michelle 

Barmann, Mark & Jan 

Barnes, Bruce 

Barnes, Lynnette 

Barnum, PhD Douglas 

Barrows, Karen 

Barsz, Bill 

Bartell, Richard 

Batze, Bonnie 

Baumgardner, John 

Beam, Craig 

Beck, Michael 

Beckwith, Diane 

Beh, Richard 

Bernache, Brenda 

Bertsch, Dr. Hans 

Biddlecome, Kelly M. 

Biggart, Neal 

Bitterling, Andrea 

Bittner, Dave 

Boland, John 

Bonamassa, Lois 

Borrelli, Rosie 

Borzik, Joette 

Bourne, Helen 

Bowlby, Eric 

Bowling, Dennis 

Boyer, David 

Boze, Bob & Sheryl 

Brady, Kristine 

Bragg, Lorie 

Bransford, Jack 

Breslauer, Ann 

Brienza, David 

Brienza, Ralph 

Bruce, Arlette 

Buffett, Brad 

Bulizak, Rose 

Burkhart, Brad 

Burleson, Charlene 

Burns, Jim 

Burrascano, Cindy 

Butler, Liza 

Butts, Nancy 

Byington, Cindy 

Cagle, Fred 

Camozzi, Josie 

Campbell, Leon 

Canedo, Karina 

Cantrell, Patricia 

Capper, Carol Ann 

Cardenas, Josefina 

Carey, Debra 

Carpenter, Raymond 

Carson, Susan & Webb 

Carvajal, Joseph 

Casady, Derek & Nancy 

Case, Ted J. 

Cassedy, Marilyn & Tim 

Cassidy, Nancy 

Cavanaugh, Jim 

Cave, Mrs. Judith 

Celso, Juanito 

Cerda, Irma 

Chacez, Lisa 

Charvet, Jan 

Chase, C.D. 

Cherney, Dan 

Chesser, Tammy 

Christian, Maria 

Christianson, Jack 

Christopherson, I. M. 

Clark, Maxine 

Cline, C. 

Cline, Sandra 

Clopp, David 

Coatsworth, Jim 

Collins, Asa 

Collins, Dr. Charles 

Collins, Dr. Tom 

Conrad, Jim 

Cook, Shirley 
Appendix B ──────────────────────────────────────────────

B-2 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Cooke, Patti 

Copelan, Jerome 

Copper, Elizabeth 

Correnti, Ruth 

Cousino, Don 

Cowling III, William 

Cox Cheryl 

Crabb David 

Cramer, Cynthia 

Crane, Jeane 

Cronk, Jim 

Crooks, Jeff 

Crouch, Laura 

Cruz, Arnie 

Cuevas, Claudia 

Curran, Gloria 

Dale, Jenica 

Dang, Emily 

Daugherty, Jim & Linda 

Davenport, Robert E. 

Davis, Bill & Shannon 

De Anda, Jr. Alfonso 

Dederick, Art 

Dedinsky, David 

DeLaurier, A. Chris 

Demarco, Darcy 

Dennison, Melissa 

Dibello-Hitta, Erica 

Dickerhoff, Wendy 

Dickey, Wayne 

Dodero, Mark 

Domingo, Maricar 

Donnelley, John 

Donovan, Christine 

Dorr, Bill 

Dougherty, Cher 

Dowell, Jeff 

Draper, Sandra 

Driscoll III, J. Gerald 

Driscoll, Joyce 

Driscoll, Thomas 

Dua, Arti 

Dudley, Joan 

Dudley, Marilyn 

Dumka, Gabrielle & Will 

Durazo, Laura 

Eastman, Joel 

Edwards, Claude 

Edwards, Willard 

Ehrlich, Shara 

Eichenlaub Jr., Carl 

Ekker, Tracey 

Ellis, Joseph M. 

Emerson, Lawrence 

Engebretson, Pam 

Esparza, Fred 

Eva, Tania 

Evans, Joyce 

Evans, Michael U. 

Fagan, Kathleen 

Farrington, Kurt & Jacki 

Fat, Thomas 

Field, Marilyn 

Fiore, David 

Fisctton, Michael 

Fisher, Dr. Robert 

Fisher, Robert A. 

Flom, Beryl 

Flores II, Rodolfo D 

Flores, Kevin 

Ford, Richard 

Fowler, Russell 

Franks, Dr. Peter 

Fraser, David 

Freedman, Michael 

Friedman, Jo 

Fuller, Susan 

Furnya, Lyn 

Gabara, Stanley 

Gaetzman, Anna 

Gailband, Charles 

Galang, Daphne 

Gallegan, Andrea 

Gallo, Paul 

Galvaw, Natalie 

Ganster, Dr. Paul 

Gates, James 

Gaylord, Tom 

Ghio, Richard 

Gilgun, Lynda 

Gill, Betsy 

Ginter, Kyle & Joann 

Gledhill, Fred 

Godshalk, Ted & Margaret 

Goethe, Wayne 

Goldman, Gayle 

Gomez, David 

Good, Deborah 

Goodrich, Roberta 

Gormican, Sue 

Grace, Don 

Griffith, Theodore 

Guerry, Melyssa 

Guilmette, Judy 

Gutierrz, Allison 

Haas, Jeremy 

Hakes, William & Joanne 

Hall, Frances 

Hallman, Lynn 

Hanna, Gail 

Hanson, Bruce 

Harmon, Wayne 

Harshberger, Linda 

Harvey, Kent 

Hatfield, Al 

Hemmingsen, Barbara 

Henderson, Teresa 

Herdt, Herman & Greida 

Hernandez, Adam 

Hernandez, Augustine 

Hernandez, Cinthia 

Hess, Carleen 

Hewitt, Cliff 

Hills, Richard 

Hinton, Mel 

Hirako, Sharon 

Hirsch, Robert 

Hoadley, Janna 

Hodgson, Patricia 

Hoffman, Connie 

Holley, John 

Hope, Charles 

Horn, Ph.D. Michael H. 

Huffman, Patricia 

Hughes, Howard 

Hugill, William 

Ikegaya, Yaz 

Inman, Sheila 

Inzunza, Gilbert 

Isaacs, Pamela 

Jackson, Wanda 

Jacoby, JoEllen 

Javor, Barbara 

Jenicks, Clinton 

Jeter, Vicky 

Jimenez, Lupita 

Johnson, Deborah 

Johnson, Elizabeth 

Johnson, William 

Johnston, Jan 

Jones, Marilyn 

Josephson, Gary 

Jungman, Bob 
Appendix B ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement B-3

Kaupp, Stephanie 

Kay, Isabelle 

Kellogg, Elizabeth 

Kelly, James 

Kelpin, Paul 

Ketchum, R. Kevin 

Kilpatrick, R. 

Klein, Michael 

Klovstad, Ann 

Knight, Debarah 

Knight, John 

Koehler, Terry 

Kraft, Mark & Vicki 

Kravitz, Ed 

Kriet, Paul & Shirley 

Kuck, Beverly 

Kuger, Christine 

Lacy, Gordon & Ruth 

Lalas, John 

Lamb, David 

Landess, Stan 

Lara, Joe 

Law, Mony 

Ledinsky, David 

Lehnert, Pat 

Leising, Adam 

Lelie, Herman & David 

Lemmo, John 

Leonardini, T. & K. 

Leslie, Eric 

Leslie, Gilda & James 

Levin, Dr. Lisa 

Lindquist, Mike 

Lineham, Marsha & Bob 

Lissner, Andrew 

Littleton, Phyllis 

Lockhart, Sharon 

Loftin, Martin 

Logsdon, William 

Lorenzen, Fred 

Loustalet, George 

Lowery, Tony 

Lubach, C. 

Lynch, Reve 

Lyons, Mik 

Maas, Phyllis 

Macias, Luis 

Mack, Callie 

Maffei, Wes 

Malley, Tom 

Mandel, Mark 

Mangan, Michele 

Mangum, Stephen 

Marogy, Danny 

Marquez, Viviane 

Martel, Lynn 

Martinez, Claudia 

Martinez, Manuel 

Martinez, Melanie 

Matticola, Phil 

Matto, Elizabeth 

Maudsley, Clare H. 

Mautino, John 

Mazur, Zeke 

Mazzola, Mary Ellen 

Mazzoni, Joe 

Mcafee, Allen 

McClelland, David 

McColl, Anne 

McCoy, Mike 

McDonald, Robert 

McIntosh, Judy 

McKirnan, Dan 

McMaster, Tim 

Meade, Jane & Pike 

Mendez, Tanya 

Merkel, Keith 

Michitzie, Rita 

Miller, Jr. James 

Mock, Dr. Patrick 

Moe, Dami 

Moe, Frank & Rhonda 

Molino, M & Elena 

Molloy, Marie 

Monroe, Dana 

Monroe, Phil 

Monsees, Edith Helen 

Moon, Owen 

Moore, Dorean & Donald 

Morgan, Jack 

Morris, Paul 

Mosczwski, Steven 

Mosher, Mary 

Moss, Marsha & Bob L. 

Movido, Jennifer 

Moya, Maria 

Mueller, Antoinette 

Muir, Marquerite 

Mulligan, Jill 

Munguia, Leticia 

Munoz, Olivia 

Mutnick, Amanda Holley 

Navarette, Henry 

Neilsen, Tom 

Nelson, Harry 

Nelson, Larry & Gail 

Nemo, William 

Nerz, Mathew 

Nicholas, Peter 

Nichols, Jean 

Nichols, Wallace 

Nielsen, Thomas 

Norberg, Robert 

Nordby, Chris 

North, Susan 

Nunez, Antonio 

Odermatt, Mary 

Opdycke, Jeff 

Opel, Don 

O'Rourke, Ruth 

Ortiz, Luzette 

Osterberg, Brian 

Owen, Wayne 

Palencia, Raejean 

Palomino, Luz 

Panos, Harry 

Pappas, Tammy 

Paris, Heidi 

Parker, Holly 

Parr, Terry 

Parystone, Stevan 

Patel, Hemant 

Patton, Robert 

Pentis, Al & Mary Anne 

Pepper, David 

Perez, Rocio 

Perez, Alberto 

Peters, Clarke 

Petitt, Terrance 

Pettit, Josephine 

Peugh, Allen 

Peugh, Jim & Barbara 

Phillips, Mike 

Phipps, Louise 

Piagentini, Dario 

Picha, Lennis 

Pickey, Wayne 

Pierce, Nuri 

Pierpoint, William 

Plant, Edward 

Player, Shannon 

Potter, Cathy 

Powers, Carolyn 
Appendix B ──────────────────────────────────────────────

B-4 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Price, Megan 

Pryde, Dr. Philip 

Puentes, Cesar 

Pulver, Sarita 

Purnell, Lorraine 

Quick, Terri 

Radinovsky, Syd/Kathy 

Ramirez, Elias 

Ramshursa, Jimmy 

Ratigan, Dr. Diane 

Rees, Jim 

Reynolds, Nick & Leslie 

Rheaume, Christine 

Richard, Lucille 

Rippel, Tasi 

Robby, Lister 

Roberts, Bes 

Roberts, Gail 

Robertson, Keith 

Robertson, Kenneth 

Robey, Steve 

Rocha, Rebecca 

Rodriguez, Eliz./Rosa 

Rodriguez, Sandra 

Roe, Bill and Laura 

Rogers, William 

Rolfe, Allison 

Romero, Connie 

Roppe, Bea 

Rosser, Anne 

Roullard, Phil 

Rowe, Reid 

Ryan, Jon 

Ryno, Marian 

Sackett, Richard 

Sanchez, Frank 

Sandoval, Rafael Bahena 

Sands, Jim 

Sannicolas, Mecaila 

Sansone, Larry 

Santos, Ramon 

Sarmiento, Mary & Steve 

Sarvis, Laura 

Sau, Luis 

Scheid, Betty J 

Scheidt, Vince 

Schmersal, Walter 

Schmidt, Brigitte 

Schneider, Carrie 

Schroeter, Steve 

Schulenberg, Judy 

Schulman, Melvyn 

Scott, Doug 

Scruggs, Jennifer 

Seay, David" 

Severns, Ken 

Shaw, Marlene & Walter 

Shenk, Art 

Shepard, Joyce 

Sherman, Craig 

Sherman, Fred 

Shirely, Ellen 

Shively, Sandra 

Sides, James 

Sierra, Arsenio 

Silliman, Ann 

Simmons, Skeet 

Simpson, Victoria 

Slahuddin, A. & N. 

Sloane, Florence 

Smith, David 

Smith, Gene 

Smith, Rodney 

Smith, Susan 

Smith, Teri 

Smothers, Ph.D. D'erdra 

Solis, Rolando & Linda 

Somers, Don 

Somerville, Jan 

Spencer, Ms. Glen 

Sproul, Fred 

Stand, Todd 

Stanton, Linda 

Stearns, Myra 

Steinhoff, Gean 

Stevens, Janet 

Steward, Dan 

Stewart, Gail 

Stewart, Lorin 

Stickel, Tracy 

Stinson, Margie 

Strickland, Carl 

Swanson Jr., Robert 

Sweeney, Marjorie 

Swift, Mitzi 

Sylvester-Gallo, Alice 

Syrjala, Edward S. 

Taliaferro, Frank 

Tange, Lora 

Tapia, Esther 

Taubbitiz, Fredericka 

Taylor, Donald 

Taylor, Harriet 

Terrazas, Octavio 

Terrones, Victor 

Thomas, Teresa 

Thorbjarnarson, Kathryn 

Tierney, Ryan 

Tindall, Russell 

Tirado, Victor 

Torbett, Glenn 

Torres, Roy 

Treppa, Ray 

Trusty, Wendy 

Tunstall, Bill 

Turner, Brian 

Uybungco, Ginny 

Van Inwegen, Earl 

Vaught, Brent 

Verbanal, Steve 

Verdugo, Carmen 

Victoria, Lorena 

Vitalich, Nicholas 

Vlassoff, Lt. 

Vonnordheim, Randy 

Wadham, Robert/Cecile 

Wages, Kent 

Wagner, Pat 

Waldrop, Kathy 

Wall, Ariadna 

Walters, Courtney 

Wasserman, Amalia 

Watry, Peter 

Watson, Becky 

Webb, Keith 

Weinberg, Jon 

Welch, Shirley 

West, Carl 

Widmann, Sabina 

Wilks Iii, John E. 

Willet, John 

Williams, Georgetta 

Wilson, Deborah 

Wilson, Lee 

Winter, Mayda 

Wolf, Joy 

Wolf, Shaura 

Wollitz, Bruce 

Wu, Julian 

Ymzon, Randy 

Yoder, Inez 

Young, Arnold 

Young, Herb 
Appendix B ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement B-5

Young, R. & G. 

Youngberg, Martha 

Zamisch, Art & Jan 

Zanoni, Richard 

Zeljecnjak, Marilyn 

Zembal, Dick 

Zetwo, Michelle 

Ziegler, Dean 

Zitlally, Reta 

Zschiesche, Peter 

Local Libraries

Chula Vista Public Libraries 

Civic Center Branch 

South Chula Vista Branch 

Coronado Public Library 

Imperial Beach Library 

National City Library 

City of San Diego Public Libraries 

Central Library, Gary Klockenga, Government Publications Librarian 

Logan Heights Branch Library 

Otay Mesa Branch Library 

Paradise Hills Branch Library 

Organizations

American Tunaboat Association 

Animal Protection Institute (C. Papouchis) 

Aqua Adventures, Kayak Center 

ATSF Railway 

Buena Vista Audubon 

Burlington Northern Santa Fe 

Cabrillo Isle Marina LLC 

California Native Plant Society 

California Waterfowl Association 

California Yacht Marina 

Camp Surf 

Center for Biological Diversity 

Center for Conservation Strategies 

Charles Company 

Chula Vista Chamber of Commerce 

Chula Vista Nature Center 

Citizens Coordinate for Century 3 

Congressional Sportsmen's Foundation 

Conservation Biology Institute 

Cooperative Alliance for Refuge 

Enhancement 

Coronado Cays Home Owners Association 

Coronado Chamber of Commerce 

Crest/Dehesa/Harbison Canyon

Crossroads II 

Defenders of Wildlife 

Downtown San Diego Partnership 

Ducks Unlimited Inc. 

Duke Energy North America 

Eagle Survey Project 

Endangered Habitats League 

Environmental Health Coalition 

Environmental Advocates 

Environmental Committee of Tijuana - S.D. 

Region 

Environmental Warriors 

Fiddler's Cove Marina 

Friends of South Bay Wildlife 

Glorietta Bay Marina 

Habitat Mitigation Committee 

Hornblower Dining Yachts 

Horned Lizard Conservation Society 

Imperial Beach Chamber of Commerce 

Kelco Company 

La Playa Yacht Club 

League for Coastal Protection 

Luce, Forward, Hamilton, & Scripps 

Manchester Resorts LP 

Mariner's Point 

Maritime Museum Association of San Diego 

Mission Bay Paddle Sports 

National Audubon Society 

National City Chamber of Commerce 

National Fish and Wildlife Foundation 

National Wildlife Federation, Western 

Natural Resources Center 

National Wildlife Refuge Association 

Navy Sailing Center 

Ocean Research International 

Otay Mesa/Nestor Planning Group 

Otay Valley Regional Park Committee 

Outboard Boating Club of San Diego 

Pacific Bell 

Palomar Audubon 
Appendix B ──────────────────────────────────────────────

B-6 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Point Reyes Bird Observatory 

Port Coronado Association 

Procopio, Cary, Hargreaves, & Savitch 

San Diego Archaeological Society 

San Diego Association of Realtors 

San Diego Association of Yacht Clubs 

San Diego Audubon Society 

San Diego Bay Committee 

San Diego Baykeeper 

San Diego Chamber of Commerce 

San Diego Council of Divers, Inc. 

San Diego County Farm Bureau 

San Diego County Fish and Game 

Association 

San Diego County Fish and Wildlife 

Advisory Commission 

San Diego Harbor Excursion 

San Diego Herp Society 

San Diego Jet Sports Club 

San Diego League of Women Voters 

San Diego Natural History Museum 

San Diego Oceans Foundation 

San Diego Personal Watercraft Association 

San Diego Railway Partnership 

San Diego River Park Foundation 

San Diego Yacht Club 

Save Our Bay Inc. 

SDG&E, Public Affairs 

Sheppard, Mullin, Richter, & Hampton LLP 

Sierra Club, San Diego Chapter 

South Bay Area Focus Team 

South Bay Boat Yard 

South Bay Salt Works 

Southwestern Wetlands Interpretive 

Association 

Southwestern College Sailing 

Southwestern Yacht Club 

Sportfishing Association of California 

Surfrider Foundation, San Diego Chapter 

Sweetwater Planning Group 

The Nature Conservancy 

The Wilderness Society 

TRVEA 

United Sportsfishers of San Diego 

WHSRN Manomet Center for Conservation 

Sciences 

Wild Coast 

Wildlife Management Institute 

Media

Eagle Newspapers 

Imperial Beach Eagle & Times 

San Diego Business Journal 

San Diego Daily Transcript 

San Diego Log 

San Diego Union-Tribune 

Star News

City Governments 

City of Chula Vista, Mayor and City Council 

City of Chula Vista, City Manager 

City of Chula Vista, Director, Community Development 

City of Chula Vista, Planning Director 

City of Chula Vista, Police Department 

City of Chula Vista, Redevelopment Projects Manager 

 City of Coronado, Mayor and City Council 

City of Coronado, City Manager 

City of Coronado, Director of Community Development 

City of Imperial Beach, Mayor and City Council 

City of Imperial Beach, City Manager 

City of Imperial Beach, Community Development Director 

City of Imperial Beach, Public Works Director 

City of Imperial Beach, Planning Department 

City of National City, Mayor and City Council 

City of National City, City Manager 

City of National City, Community Development 

City of National City, Planning Director 

City of San Diego, Mayor and City Council 
Appendix B ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement B-7

City of San Diego, City Manager 

City of San Diego, Community Planning 

City of San Diego, Engineering and Capital Projects 

City of San Diego, Environmental Services 

City of San Diego, Metropolitan Wastewater 

City of San Diego, Multiple Species Conservation Planning 

City of San Diego, Park and Recreation Department 

City of San Diego, Police Department 

City of San Diego, Real Estate Assets Department 

County Government

San Diego County Supervisor Greg Cox 

San Diego County Supervisor Dianne Jacob 

San Diego County Supervisor Ron Roberts 

County of San Diego, Real Property Division 

County of San Diego, Environmental Health Services 

County of San Diego, Parks and Recreation Department 

County of San Diego, Department of Planning and Land Use 

County of San Diego, Department of Public Works 

Other Local Agencies 

California American Water Company 

Center City Development Corporation - Public Works Department 

Harbor Patrol, Dave Hall, Chief of Harbor Police 

International Border Water Commission 

Metropolitan Transit Development Board (MTDB) 

Otay Water District 

San Diego County Airport Authority 

San Diego Association of Governments (SANDAG) 

South Bay Irrigation District 

Sweetwater Authority 

Tijuana Valley Company Water District 

Unified Port of San Diego 

California State Agencies

Cal EPA 

California Coastal Commission, Executive Director, Peter Douglas 

California Coastal Commission, Federal Consistency, James Raives 

California Coastal Commission, San Diego Coast District 

California Coastal Conservancy 

California Department of Forestry 

California Fish and Game Commission 

California State Parks, State Historic Preservation Officer 

California State Parks, Superintendent, Ronilee Clark 

Caltrans, District 11 

Department of Boating and Waterways, Director, Raynor T. Tsuneyoshi 

Department of Conservation 

Department of Fish and Game, Director, Ryan Broddrick 

Department of Fish and Game, Marilyn Fluharty 

Department of Fish and Game, South Coast Regional Manager, Charles Raysbrook 
Appendix B ──────────────────────────────────────────────

B-8 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Resources Agency, Secretary, Mike Chrisman 

San Diego Regional Water Quality Control Board, Region 9, Executive Officer, John Robertus 

San Diego Regional Water Quality Control Board, Region 9, Pete Michael 

State Lands Commission, Executive Officer, Paul Thayer 

State Water Resources Control Board, Arthur G. Baggett Jr., Chair 

Wetlands Recovery Project 

Wildlife Conservation Board 

Tribal Governments

Barona Band of Mission Indians 

Campo Band of Mission Indians 

Cuyapaipe Community of Diegueno Mission Indians 

Inaja Band of Mission Indians 

Jamul Indian Village 

La Jolla Band of Luiseno Indians 

La Posta Band of Mission Indians 

Los Coyotes Reservation

Manzanita Tribe of Kumeyaay Indians 

Mesa Grande Band of Indians 

Pala Band of Mission Indians 

Pauma Band of Mission Indians 

Rincon Indian Reservation 

San Pasqual Band of Indians 

Santa Ysabel Indian Reservation 

Sycuan Band of Indians 

Viejas Reservation 

Carmen Lucas 

Jim Velasques 

Kumeyaay Cult. Repatriation Committee 

Kumeyaay Cultural Heritage Preservation 

Kumeyaay Cultural Historic Committee 

Federal Agencies & Offices

EIS Filing Section US Environmental Protection Agency, Office of Federal Activities 

FAA - ARPT DIV AWP-600 

National Interagency Fire Center 

NOAA Marine Fisheries, Bob Hoffman 

U.S. Army, Corps of Engineers 

U.S. Border Patrol, San Diego Sector 

U.S. Coast Guard, Marine Safety Office 

U.S. Coast Guard, Port Operations 

U.S. Department of the Interior, Office of Environmental Policy and Compliance, Phyllis Davis 

U.S. Department of Transportation, Federal Highway Administration 

U.S. Environmental Protection Agency, Paul Michael 

U.S. Environmental Protection Agency, Region 9 

U.S. Geological Survey 

U.S. Navy, Naval Facilities Engineering Command 

U.S. Navy, Southwest Division, NAVFAC, Natural Resources Department, Mitch Perdue 

U.S. Navy, Southwest Division, NAVFAC, Natural Resources Department, Tamara Conkle 

USDA, APHIS, Wildlife Services, District Supervisor, John Turman 

USDA, Natural Resource Conservation District of Greater San Diego County 
Appendix B ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement B-9

USFWS 

Bellantoni, Liz, USFWS, Chief, Planning and Policy 

Bohan, Carolyn, USFWS, National Wildlife Refuge System 

Bortner, Brad, USFWS, Migratory Birds & Habitat Programs 

Concannon, Julie, USFWS, Region 1, NEPA Coordinator 

Drescher, Dave, USFWS, Region 1, Refuge Planning-Cartography/GIS 

Fuller, Nell, USFWS, Region 1, Refuge Support, Policy 

Hadley, Richard, USFWS, CNO, Assistant Refuge Supervisor 

Harrison, Ben, USFWS, Region 1, Land Protection Planning 

Harrison, Jean, USFWS, Region 1, Division of Visitor Services 

Houghten, Chuck, USFWS, Division of Refuge Planning 

Kier-Haggenjos, Kay, USFWS, Region 1, Division of Refuge Planning 

Kilbride, Kevin USFWS Refuge Biology 

Kolar, Marge, USFWS, Assistant Manager of Refuges 

Marxen, Mike, USFWS, Region 1, Division of Refuge Planning 

McAdams, Amanda, USFWS, Fire Planner 

Moore, Stephen USFWS, Region 1, Refuge Operations Support 

Paveglio, Fred USFWS, Refuge Biology 

Pavusko, Gary, USFWS, CNO, Fire Management Officer 

Pelz, Mark USFWS CA/NV Refuge Planning 

Rauch, Paul, USFWS, Engineering 

Raymond, Anan, USFWS, Region 1, Cultural Resources Team 

Saul, Susan, USFWS, External Affairs Office 

Shaffer, Robert, USFWS, Joint Venture Coordinator 

Sheppard, Cathy, USFWS, Region 1, Division of Realty 

Smiley, Tom, USFWS, Engineering 

Sobiech, Scott USFWS, Contaminants 

Speulda, Lou Ann, USFWS, Cultural Resources Branch 

Thompson, Steve, USFWS, Manager 

Walsworth, Dan, USFWS, Refuge Supervisor 

Zimmerman, Tara, USFWS, Migratory Birds & Habitat Programs 

U.S. Congress

Honorable Barbara Boxer, U.S. Senate 

Honorable Dianne Feinstein, U.S. Senate 

Congresswoman Susan Davis, 53th District 

Congressman Bob Filner, 51th District 

California State Legislature

Governor Arnold Schwarzenegger 

Lieutenant Governor Cruz Bustamante

State Senator Dede Alpert, 39th District 

State Assemblyman Juan Vargas, 79th District 

State Assemblywoman Christine Kehoe, 76th District 

State Assemblywoman Shirley Horton, 78th District 
Appendix B ──────────────────────────────────────────────

B-10 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

2. Distribution List for the Final Comprehensive Conservation 

Plan/Environmental Impact Statement

The individuals, organizations, local businesses, Tribal governments, interested 

media, public agencies, and elected officials listed above as receiving notification of 

the draft CCP/EIS also received notice of the availability of the Final CCP/EIS unless 

they were subsequently removed from the distribution list at their request or because 

the Post Office was unable to deliver a notice to the address of record. The following 

additional individuals and other interested parties received notice of the availability 

of the Final CCP/EIS. 

California State Legislature

State Senator Christine Kehoe, 39th District 

State Assemblywoman Lori Saldana, 76th District

Organizations

Johnson & Hanson LLP

Individuals

Brian Foster

Kirsten Winter

Guy McCaskie

Therese Clawson

Kenneth Weaver

Susan Yamagata

Jack Daynes

Nils Warnock

Theresa Jancek

B. Sachau

The following libraries were provided with a complete set of the Final CCP/EIS:

Chula Vista Public Libraries

Civic Center Branch

South Chula Vista Branch

Coronado Public Library

Imperial Beach Library

National City Library

City of San Diego Public Libraries

Central Library, Gary Klockenga, Government Publications Librarian

Otay Mesa Branch Library 
 

Appendix C 

 Bird Species Lists
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement C-1

Appendix C: Bird Species Lists 

The following lists include bird species that have been observed at least once on the specified 

Refuge Unit. The birds' common and scientific names are provided in accordance with the 7th 

edition (1998) of the A. O. U. Checklist of North American Birds. (* Indicates bird species known 

to nest on the refuge.) 

Sweetwater Marsh Unit 

Common Name Scientific Name

Red-throated Loon Gavia stellata 

Pacific Loon Gavia pacifica

Common Loon Gavia immer

Pied-billed Grebe Podilymbus podiceps 

Horned Grebe Podiceps auritus 

Eared Grebe Podiceps nigricollis 

Western Grebe Aechmophorus occidentalis 

Clark’s Grebe Aechmophorus clarkii

American White Pelican Pelecanus erythrorhynchos 

Brown Pelican Pelecanus occidentalis 

Double-crested Cormorant Phalacrocorax auritus 

Pelagic Cormorant Phalacrocorax pelagicus

Great Blue Heron Ardea herodias 

Great Egret Ardea alba 

Snowy Egret Egretta thula 

Little Blue Heron Egretta caerulea 

Tricolored Heron Egretta tricolor

Reddish Egret Egretta rufescens

Green Heron Butorides virescens 

Black-crowned Night Heron Nycticorax nycticorax 

White-faced Ibis Plegadis chihi 

Turkey Vulture Cathartes aura

Snow Goose Chen caerulescens 

Ross's Goose Chen rossii

Canada Goose Branta Canadensis 

Brant Branta bernicla 

Gadwall Anas strepera 

Eurasian Wigeon Anas penelope

American Wigeon Anas americana 

Mallard Anas platyrhynchos 

Blue-winged Teal Anas discors 

Cinnamon Teal Anas cyanoptera 

Northern Shoveler Anas clypeata 

Northern Pintail Anas acute 

Green-winged Teal Anas crecca 

Canvasback Aythya valisineria 

Redhead Aythya americana 
Appendix C ──────────────────────────────────────────────

C-2 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Ring-necked Duck Aythya collaris 

Greater Scaup Aythya marila 

Lesser Scaup Aythya affinis 

Surf Scoter Melanitta perspicillata 

White-winged Scoter Melanitta fusca 

Black Scoter Melanitta nigra

Long-tailed Duck Clangula hyemalis 

Bufflehead Bucephala albeola 

Common Goldeneye Bucephala clangula 

Hooded Merganser Lophodytes cucullatus

Red-breasted Merganser Mergus serrator 

Ruddy Duck Oxyura jamaicensis 

Osprey Pandion haliaetus 

White-tailed Kite Elanus leucurus 

Bald Eagle Haliaeetus leucocephalus 

Northern Harrier Circus cyaneus 

Sharp-shinned Hawk Accipiter striatus 

Cooper's Hawk Accipiter cooperii 

Red-shouldered Hawk Buteo lineatus 

Swainson's Hawk Buteo swainsoni 

Red-tailed Hawk Buteo jamaicensis 

Ferruginous Hawk Buteo regalis 

Golden Eagle Aquila chrysaetos 

Crested Caracara Caracara cheriway 

American Kestrel* Falco sparverius 

Merlin Falco columbarius 

Peregrine Falcon Falco peregrinus 

Prairie Falcon Falco mexicanus 

California Quail Callipepla californica 

Light-footed Clapper Rail* Rallus longirostris levipes 

Virginia Rail Rallus limicola 

Sora Porzana Carolina 

Common Moorhen Gallinula chloropus

American Coot Fulica americana 

Black-bellied Plover Pluvialis squatarola 

Pacific-golden Plover Pluvialis fulva 

Western Snowy Plover* Charadrius alexandrinus nivosus

Semipalmated Plover Charadrius semipalmatus 

Killdeer* Charadrius vociferous 

Mountain Plover Charadrius montanus

Black-necked Stilt Himantopus mexicanus 

American Avocet Recurvirostra americana 

Greater Yellowlegs Tringa melanoleuca 

Willet Tringa semipalmatus

Lesser Yellowlegs Tringa flavipes 

Spotted Sandpiper Actitis macularia 

Whimbrel Numenius phaeopus 

Long-billed Curlew Numenius americanus 

Marbled Godwit Limosa fedoa 
Appendix C ──────────────────────────────────────────────

────────────── Final Comprehensive Conservation Plan/Environmental Impact Statement C-3

Ruddy Turnstone Arenaria interpres

Black Turnstone Arenaria melanocephala

Surfbird Aphriza virgata 

Red Knot Calidris canutus 

Sanderling Calidris alba 

Semipalmated Sandpiper Calidris pusilla 

Western Sandpiper Calidris mauri 

Least Sandpiper Calidris minutilla 

Dunlin Calidris alpine 

Stilt Sandpiper Calidris himantopus 

Ruff Philomachus pugnax

Short-billed Dowitcher Limnodromus griseus 

Long-billed Dowitcher Limnodromus scolopaceus 

Common Snipe Gallinago gallinago 

Wilson's Phalarope Phalaropus tricolor 

Red-necked Phalarope Phalaropus lobatus 

Parasitic Jaeger Stercorarius parasiticus 

Franklin's Gull Larus pipixcan 

Bonaparte's Gull Larus philadelphia 

Heermann's Gull Larus heermanni 

Mew Gull Larus canus 

Ring-billed Gull Larus delawarensis 

California Gull Larus californicus 

Herring Gull Larus argentatus 

Thayer's Gull Larus thayeri 

Western Gull Larus occidentalis 

Glaucous-winged Gull Larus glaucescens 

Black Skimmer Rynchops niger

California Least Tern* Sternula antillarum

Gull-billed Tern Gelochelidon nilotica

Caspian Tern Hydroprogne caspia

Forster's Tern* Sterna forsteri 

Royal Tern Thalasseus maximus

Elegant Tern Thalasseus elegans

Rock Dove Columba livia 

Mourning Dove* Zenaida macroura 

Greater Roadrunner Geococcyx californianus 

Barn Owl Tyto alba 

Great Horned Owl Bubo virginianus 

Burrowing Owl* Athene cunicularia 

Short-eared Owl Asio flammeus 

Lesser Nighthawk Chordeiles acutipennis

Common Nighthawk Chordeiles minor 

Vaux's Swift Chaetura vauxi 

White-throated Swift Aeronautes saxatalis 

Black-chinned Hummingbird Archilochus alexandri

Anna’s Hummingbird* Calypte anna 

Costa's Hummingbird* Calypte costae 

Rufous Hummingbird Selasphoras rufus 

Allen's Hummingbird Selasphorus sasin

Belted Kingfisher Ceryle alcyon 
Appendix C ──────────────────────────────────────────────

C-4 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Northern Flicker Colaptes auratus 

Western Wood-Pewee Contopus sordidulus 

Willow Flycatcher Empidonax traillii 

Pacific-slope Flycatcher Empidonax difficilis 

Black Phoebe Sayornis nigricans

Say's Phoebe Sayornis saya

Ash-throated Flycatcher Myiarchus cinerascens 

Cassin's Kingbird Tyrannus vociferans

Western Kingbird Tyrannus verticalis 

Loggerhead Shrike* Lanius ludovicianus 

Blue-headed Vireo Vireo solitarius

Warbling Vireo Vireo gilvus 

Western Scrub Jay Aphelocoma californica 

American Crow Corvus brachyrhynchos 

Common Raven Corvus corax 

Magpie Jay Calocitta formosa

Horned Lark* Eremophila alpestris 

Tree Swallow Tachycineta bicolor 

Violet-green Swallow Tachycineta thalassina 

Northern Rough-winged Swallow Stelgidopteryx serripennis 

Cliff Swallow Petrochelidon pyrrhonota 

Barn Swallow Hirundo rustica 

Bushtit* Psaltriparus minimus 

Cactus Wren Campylorhynchus brunneicapillus

Bewick's Wren* Thryomanes bewickii 

House Wren Troglodytes aedon 

Marsh Wren Cistothorus palustris 

Ruby-crowned Kinglet Regulus calendula 

Blue-gray Gnatcatcher Polioptila caerulea 

California Gnatcatcher Polioptila californica

Mountain Bluebird Sialia currucoides 

Swainson's Thrush Catharus ustulatus

Hermit Thrush Catharus guttatus 

American Robin Turdus migratorius 

Wrentit Chamaea fasciata

Northern Mockingbird* Mimus polyglottos 

Sage Thrasher Oreoscoptes montanus 

California Thrasher Toxostoma redivivum 

European Starling* Sturnus vulgaris 

Red-throated Pipit Anthus cervinus

American Pipit Anthus rubescens 

Cedar Waxwing Bombycilla cedrorum 

Phainopepla Phainopepla nitens 

Orange-crowned Warbler Vermivora celata 

Nashville Warbler Vermivora ruficapilla

Yellow Warbler Dendroica petechia 

Magnolia Warbler Dendroica magnolia

Yellow-rumped Warbler Dendroica coronata 

Black-throated Gray Warbler Dendroica nigrescens 

MacGillivray's Warbler Oporornis tolmiei 

Common Yellowthroat Geothlypis trichas 
Appendix C ──────────────────────────────────────────────

────────────── Final Comprehensive Conservation Plan/Environmental Impact Statement C-5

Wilson's Warbler Wilsonia pusilla 

Western Tanager Piranga ludoviciana 

Green-tailed Towhee Pipilo chlorurus

Spotted Towhee Pipilo maculatus 

California Towhee Pipilo crissalis 

Vesper Sparrow Pooecetes gramineus 

Lark Bunting Calamospiza melanocorys

Savannah Sparrow Passerculus sandwichensis

Belding’s Savannah Sparrow* Passerculus sandwichensis beldingi 

Large-billed Savannah Sparrow Passerculus sandwichensis rostratus 

Grasshopper Sparrow Ammodramus savannarum 

Nelson's Sharp-tailed Sparrow Ammodramus nelsoni

Song Sparrow* Melospiza melodia 

Lincoln's Sparrow Melospiza lincolnii 

Swamp Sparrow Melospiza georgiana

White-crowned Sparrow* Zonotrichia leucophrys 

Golden-crowned Sparrow Zonotrichia atricapilla 

Dark-eyed Junco Junco hyemalis 

Blue Grosbeak Guiraca caerulea 

Lazuli Bunting Passerina amoena 

Red-winged Blackbird Agelaius phoeniceus 

Tricolored Blackbird Agelaius tricolor 

Western Meadowlark* Sturnella neglecta 

Yellow-headed Blackbird Xanthocephalus xanthocephalus

Brewer's Blackbird Euphagus cyanocephalus 

Great-tailed Grackle Quiscalus mexicanus

Brown-headed Cowbird Molothrus ater 

Hooded Oriole Icterus cucullatus 

Bullock’s Oriole Icterus bullockii 

House Finch* Carpodacus mexicanus 

Lesser Goldfinch Carduelis psaltria 

Lawrence's Goldfinch Carduelis lawrencei 

American Goldfinch Carduelis tristis 

House Sparrow* Passerculus domesticus 

(Source: Chula Vista Nature Center 1998 and Merkel & Associates, Inc. 2000b) 

South San Diego Bay Unit 

Common Name Scientific Name 

Red-throated Loon Gavia stellata 

Common Loon Gavia immer

Pied-billed Grebe Podilymbus podiceps 

Horned Grebe Podiceps auritus 

Eared Grebe Podiceps nigricollis 

Western Grebe Aechmophorus occidentalis 

Clark’s Grebe Aechmophorus clarkii

American White Pelican Pelecanus erythrorhynchos 

Brown Pelican Pelecanus occidentalis 

Double-crested Cormorant* Phalacrocorax auritus 
Appendix C ──────────────────────────────────────────────

C-6 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Great Blue Heron Ardea herodias 

Great Egret Ardea alba 

Snowy Egret Egretta thula 

Little Blue Heron Egretta caerulea 

Tricolored Heron Egretta tricolor

Reddish Egret Egretta rufescens

Green Heron Butorides virescens 

Black-crowned Night Heron Nycticorax nycticorax 

White-faced Ibis Plegadis chihi

Snow Goose Chen caerulescens 

Brant Branta bernicla 

Gadwall* Anas strepera 

American Wigeon Anas americana 

Mallard* Anas platyrhynchos 

Blue-winged Teal Anas discors 

Cinnamon Teal Anas cyanoptera 

Northern Shoveler Anas clypeata 

Northern Pintail Anas acute 

Green-winged Teal Anas crecca 

Redhead Aythya americana 

Ring-necked Duck Aythya collaris 

Greater Scaup Aythya marila 

Lesser Scaup Aythya affinis 

Surf Scoter Melanitta perspicillata 

Long-tailed Duck Clangula hyemalis 

Bufflehead Bucephala albeola 

Common Goldeneye Bucephala clangula 

Common Merganser Mergus merganser 

Red-breasted Merganser Mergus serrator 

Ruddy Duck Oxyura jamaicensis 

Osprey Pandion haliaetus 

White-tailed Kite Elanus leucurus 

Northern Harrier Circus cyaneus 

Sharp-shinned Hawk Accipiter striatus 

Cooper's Hawk Accipiter cooperii 

Red-tailed Hawk Buteo jamaicensis 

American Kestrel Falco sparverius 

Merlin Falco columbarius 

Peregrine Falcon Falco peregrinus 

Light-footed Clapper Rail* Rallus longirostris levipes

American Coot Fulica americana 

Black-bellied Plover Pluvialis squatarola 

American Golden Plover Pluvialis dominica 

Western Snowy Plover* Charadrius alexandrinus nivosus

Semipalmated Plover Charadrius semipalmatus 

Killdeer* Charadrius vociferus 

Black-necked Stilt* Himantopus mexicanus 

American Avocet* Recurvirostra americana 

Greater Yellowlegs Tringa melanoleuca 

Willet Tringa semipalmatus 
Appendix C ──────────────────────────────────────────────

────────────── Final Comprehensive Conservation Plan/Environmental Impact Statement C-7

Lesser Yellowlegs Tringa flavipes 

Spotted Sandpiper Actitis macularia 

Whimbrel Numenius phaeopus 

Long-billed Curlew Numenius americanus 

Marbled Godwit Limosa fedoa 

Ruddy Turnstone Arenaria interpres

Black Turnstone Arenaria melanocephala

Surfbird Aphriza virgata 

Red Knot Calidris canutus 

Sanderling Calidris alba 

Western Sandpiper Calidris mauri 

Least Sandpiper Calidris minutilla 

Pectoral Sandpiper Calidris melanotos 

Dunlin Calidris alpina 

Short-billed Dowitcher Limnodromus griseus 

Long-billed Dowitcher Limnodromus scolopaceus 

Wilson's Phalarope Phalaropus tricolor 

Red-necked Phalarope Phalaropus lobatus 

Red Phalarope Phalaropus fulicaria 

Parasitic Jaeger Stercorarius parasiticus 

Franklin's Gull Larus pipixcan 

Bonaparte's Gull Larus philadelphia 

Heermann's Gull Larus heermanni 

Mew Gull Larus canus 

Ring-billed Gull Larus delawarensis 

California Gull Larus californicus 

Herring Gull Larus argentatus 

Western Gull* Larus occidentalis 

Glaucous-winged Gull Larus glaucescens 

Black Skimmer* Rynchops niger

California Least Tern* Sternula antillarum

Gull-billed Tern* Gelochelidon nilotica

Caspian Tern* Hydroprogne caspia

Black Tern Chlidonias niger 

Common Tern Sterna hirundo

Forster's Tern* Sterna forsteri 

Royal Tern* Thalasseus maximus

Elegant Tern* Thalasseus elegans

Rock Dove Columba livia 

Mourning Dove Zenaida macroura 

Greater Roadrunner Geococcyx californianus 

Barn Owl Tyto alba 

Burrowing Owl Athene cunicularia 

Short-eared Owl Asio flammeus 

Anna’s Hummingbird Calypte anna 

Belted Kingfisher Ceryle alcyon 

Black Phoebe Sayornis nigricans 

Ash-throated Flycatcher Myiarchus cinerascens

Western Kingbird Tyrannus verticalis 

Loggerhead Shrike Lanius ludovicianus 

American Crow Corvus brachyrhynchos 
Appendix C ──────────────────────────────────────────────

C-8 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

Common Raven Corvus corax

Horned Lark* Eremophila alpestris 

Tree Swallow Tachycineta bicolor 

Northern Rough-winged Swallow Stelgidopteryx serripennis 

Cliff Swallow Petrochelidon pyrrhonota 

Barn Swallow Hirundo rustica 

Bushtit Psaltriparus minimus 

Marsh Wren Cistothorus palustris 

Northern Mockingbird Mimus polyglottos

European Starling Sturnus vulgaris 

American Pipit Anthus rubescens 

Yellow-rumped Warbler Dendroica coronata 

Common Yellowthroat Geothlypis trichas 

Wilson's Warbler Wilsonia pusilla 

California Towhee Pipilo crissalis 

Belding’s Savannah Sparrow* Passerculus sandwichensis beldingi 

Song Sparrow Zonotrichia leucophrys 

Blue Grosbeak Guiraca caerulea 

Red-winged Blackbird Agelaius phoeniceus 

Western Meadowlark Sturnella neglecta 

Brewer's Blackbird Euphagus cyanocephalus 

Hooded Oriole Icterus cucullatus 

House Finch Carpodacus mexicanus 

Lesser Goldfinch Carduelis psaltria 

House Sparrow Passer domesticus 

(Source: City of San Diego 1987, USFWS 1994, US Navy 2000, Tierra Environmental Services 

2001, and Tony Stands, pers. comm., April 2004) 
 

Appendix D 

 CCP Implementation
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-1

Appendix D: CCP Implementation 

A. Introduction

The Final Comprehensive Conservation Plan (CCP) for the San Diego Bay National Wildlife 

Refuge will be prepared following approval of the Final EIS and issuance of the Record of Decision 

(ROD), which will identify the proposed action. This appendix combined with Chapters 1 and 3 and 

portions of Chapter 2 of the Final CCP/EIS will form the basis for the Final CCP. Implementation 

of the CCP can begin following the issuance of the ROD. Although it is our intent to implement the 

proposed strategies (projects) by the established deadlines, the timing of implementation may vary 

depending upon a variety of factors, including funding, staffing, compliance with Federal 

regulations, partnerships, and the results of monitoring and evaluation. Some strategies, such as 

those related to habitat restoration, will require the completion of step-down plans and appropriate 

environmental compliance documents before they can be implemented. This appendix will further 

define how implementation of the preferred alternatives for both the Sweetwater Marsh Unit and 

the South San Diego Bay Unit (described in Chapter 2) would proceed if they are identified as the 

proposed action in the ROD. 

B. Implementation Overview

During the 15 years following CCP approval, the CCP will serve as the primary reference 

document for all Refuge planning, operations, and management. Presented in Tables D-1 and D-2 

are the priorities for implementing the various wildlife and habitat management and visitor 

services (public use) strategies described in the preferred alternatives for the Sweetwater Marsh 

and South San Diego Bay Units. Completion of any of these actions would however be dependent 

upon the various factors discussed above and the order of implementation could change if funds for 

a specific project are identified earlier than anticipated. These strategies would be implemented 

with assistance from new and existing partners, including public agencies, non-governmental 

organizations, and the public. Consistent public outreach and continued coordination with Refuge 

constituents are essential components of this implementation process. Some of the partnership 

opportunities to be explored during the 15-year life of this CCP are described below, as are the 

projects, monitoring responsibilities, and staffing and funding requirements needed to successfully 

implement the CCP. 

 

CCPs are intended to evolve with each Refuge, and the Improvement Act specifically requires that 

these plans be formally revised and updated at least every 15 years. The formal revision process 

will follow the same steps as those implemented for the initial CCP development process, with a 

major emphasis placed on public involvement. Until a formal revision is initiated, the Service will 

periodically review and update the CCP (at least as often as every five years) to address needs 

identified as a result of monitoring or in response to adaptive management procedures. This CCP 

will also be informally reviewed by Refuge staff while preparing annual work plans and updating 

the Refuge databases. It may also be reviewed during routine inspections or programmatic 

evaluations. Results of any or all of these reviews may indicate a need to modify the plan. The 

goals described in this CCP will not change until they are reevaluated as part of the formal CCP 

revision process. However, the objectives and strategies may be revised to better address 

changing circumstances or to take advantage of increased knowledge of Refuge resources. If 

revisions to the CCP are required prior to the initiation of formal revisions, the level of public 

involvement and associated NEPA documentation will be determined by the Refuge Manager. 
Appendix D ──────────────────────────────────────────────

 D-2 San Diego Bay National Wildlife Refuge ───────────────────────────────

Table D-1

San Diego Bay National Wildlife Refuge

Prioritized List of Wildlife and Habitat Management Projects*

Priority Unit Description 

1 SSDB Phase 1 - Salt Pond Restoration: 

 a. Step-down planning and detailed engineering 

 b. Restore tidal influence to Pond 11 

 c. Restore tidal influence to Ponds 10 and 10A 

2 SSDB Phase 2 - Nesting Enhancements within the Salt Pond Complex: 

 a. Step-down planning and detailed engineering 

 b. Phased development of new nesting sites 

 c. Enhance nesting substrate 

 d. Reconfigure pond levees 

3 SSDB Otay River Floodplain Restoration: 

 a. Step-down planning and detailed engineering 

 b. Implement restoration plan 

4 SSDB Phase 2 Salt Pond Restoration: 

 a. Step-down planning and detailed engineering 

 b. Restore tidal influence to Ponds 12-15 

 c. Restore tidal influence to Ponds 23-25 and 28-30 

 d. Initiate the managed water system 

 e. Prepare Pond 44 for seabird nesting habitat 

5 SWM Restore wetland habitat at the F&G Street Marsh: 

 a. Step-down planning and detailed engineering 

 b. Implement wetland habitat restoration 

 c. Address contaminant issues at F&G Street Marsh 

6 SWM Improve tidal circulation within Paradise Marsh: 

 a. Address contaminant issues in Paradise Marsh 

 b. Step-down planning and detailed engineering to remove or lower existing weir 

 c. Remove or lower the existing weir 

7 SWM Improve tidal circulation within Sweetwater Marsh: 

 a. Step-down planning and detailed engineering to improve tidal circulation 

 b. Add new culvert in the existing access road 

 c. Remove old access road

 d. Address sediment accumulation in existing tidal channels 

 e. Lower berm south of Gunpowder Point

8 SWM Enhance D Street fill to improve nesting habitat quality and fledgling access: 

 a. Step-down planning for substrate enhancement/improved fledgling access to foraging areas 

 b. Implement nesting substrate enhancements 

9 SWM Improve access between nesting and foraging areas on the D Street Fill

10 SWM Restore native upland and wetland habitat on Gunpowder Point: 

 a. Step-down planning for habitat restoration 

 b. Implement upland habitat restoration 

 c. Implement wetland habitat restoration along the northern edge of Gunpowder Point 

11 SSDB Identify Long Term Funding for Predator Management in tern and plover nesting areas 

12 SWM Identify Long Term Funding for Predator Management in tern and plover nesting areas 

* Restoration priorities may change or implementation may be accelerated if funding for a specific project is 

identified sooner than anticipated. 
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-3

Table D-2

San Diego Bay National Wildlife Refuge

Prioritized List of Visitor Services Projects

Priority Unit Description 

1 SSDB Increase Opportunities for Wildlife Observation/Interpretation: 

 a. Increase the number of guided tours within the salt pond complex 

 b. Conduct step-down planning for pedestrian pathway and interpretation along south boundary 

 c. Construct the pedestrian pathway from 7th to 10th Street 

 d. Develop an interpretive overlook at the end of 10th Street 

 e. Develop an observation deck at the end of 8th Street 

 f. Construct the pedestrian pathway from Florida Street to 13th Street

 g. Construct an observation overlook in the vicinity of Florida Street 

 h. Design and Construct an interpretive trail around Pond 28 

 i. Design and implement an interpretive program about the history of hunting in San Diego Bay

2 SWM Improve Opportunities for Wildlife Observation and Environmental Interpretation: 

 a. Step-down planning for interpretive trail on Gunpowder Point 

 b. Realign the existing trail 

 c. Design and install new interpretive signs 

 d. Work with National City and Chula Vista to provide environmental interpretation 

3 SSDB Expand the existing Habitat Heroes Environmental Education Program consistent with the CCP 

4 SWM Develop public outreach plan to reduce disturbance from adjacent areas 

5 SWM Develop public outreach plan to reduce wildlife disturbance in the open waters of the Refuge 

6 SWM Develop a Cultural Resource Management Plan for this Unit 

7 SSDB Develop a Cultural Resource Management Plan for this Unit 

C. Wildlife and Habitat Management

The preferred alternatives for the Sweetwater Marsh and South San Diego Bay Units include a 

variety of wildlife and habitat management “strategies” or projects that when implemented will

meet the goals and objectives outlined in the CCP. The timing for implementation of these 

projects is driven by the Service’s trust responsibilities (i.e., endangered and threatened species, 

migratory birds), the mission of the Refuge system, Refuge purposes, and the availability of 

funding. The best science available will be used to measure the effectiveness of these projects in 

achieving the goals and objectives for the Refuge. 

Past management on the Refuge has been focused on maintaining appropriate nesting habitat for 

seabirds, implementing predator control to protect listed species, and minimizing disturbance to 

resident and migratory bird populations. While these management practices would continue or be 

expanded (e.g., nesting substrate enhancement and nesting area expansion projects), additional 

management actions would be implemented as funding permits. Additional focus would be placed 

on the inventory and monitoring of the various species and habitats supported on the Refuge. As 

described below, considerable emphasis would be placed on habitat enhancement and restoration 

to benefit native wildlife and plant species. 

Habitat Enhancement and Restoration

Various enhancement and restoration projects are described in the CCP that once 

implemented would expand and/or improve the overall habitat value of this Refuge for a 

variety of species. Full restoration of the structure and function of the coastal wetland 

habitats proposed within the CCP particularly for the South San Diego Bay Unit may not 
Appendix D ──────────────────────────────────────────────

 D-4 San Diego Bay National Wildlife Refuge ───────────────────────────────

be achieved within the 15-year life of this plan, however, the direction provided in the CCP 

will ensure that significant strides towards the goal of providing fully functional, high value 

habitat for migratory birds and listed species such as the light-footed clapper rail, 

California least tern, and western snowy plover will be achieved. 

 

Implementation of some of the projects would involve minimal effort such as removing or 

lowering the weir near Paradise Marsh, while restoration of the salt ponds in the South 

San Diego Bay Unit would require completion of additional studies, coordination with a 

variety of partners, preparation of final engineering and restoration plans, approval of 

various permits, and funding for both step-down planning and implementation. 

Restoration of tidal influence within the majority of the salt ponds on the South San Diego 

Bay Unit could be implemented under several scenarios, as described in Chapter 2. One of 

the scenarios would involve a phased approach to restoration. The details of such a phased 

approach are presented below.

Salt Pond Restoration Phasing Plan

Phase 1 - Implement Restoration of the Western Ponds (Ponds 10, 10A, and 11) 

and Initiate Nesting Enhancement Projects throughout the Salt Works

Years 1, 2, and 3 – Studies, Final Restoration Planning, and Permitting

• Prepare a work plan outlining the various studies to be conducted prior to 

restoring tidal influence to the salt ponds. Studies would include, but are not 

limited to:

o Characterization of the pond sediments (e.g., grain size, salinity levels, 

presence of any contaminants)

o Collection of data regarding avifauna abundance, diversity, use, and 

distribution within the salt ponds and the adjacent mudflats

o Identification of the invertebrates present within the various ponds

o Analysis of material to be used for new nesting areas and/or for 

optimizing pond elevations to achieve desired habitat types

• Provide opportunities for public input during final restoration planning and 

host annual public workshops to provide for public input throughout the 

restoration process

• Explore and promote scientific research opportunities with various 

universities, USGS, and others that would begin in Year 1 and extend through 

the life of the project, as appropriate

• Design any water control structures, bridges, and levee protection measures 

that would be required following restoration of tidal influence into the ponds 

• Prepare final engineering/restoration plans incorporating as appropriate the 

results of the tasks described above 

• Design a monitoring plan for Pond 11

• Obtain all necessary permits and complete environmental compliance reviews
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-5

Year 4 – Prepare for and Restore Tidal Influence in Pond 11/Begin Nesting 

Enhancements 

• Prepare Pond 11 for restoration:

o Remove Pond 11 from the salt production system and make the 

necessary changes to the system to allow water to move from Pond 10 

into Pond 12

o Reconfigure the pond elevations per final engineering plans (this may 

involve moving material from Pond 10 to Pond 11, transporting 

material from the Otay River floodplain into Pond 11, or simply 

recontouring the pond to achieve the desired elevations)

• Restore tidal influence to Pond 11 in accordance with approved 

engineering/restoration plans

• Begin implementing nesting habitat enhancements including recontouring 

existing levees, widening some levees, and preparing new nesting areas within 

existing ponds

• Initiate monitoring of Pond 11 (e.g., monitor invertebrate, fish, and plant 

colonization, water quality, and possible presence of invasive species in 

restored Pond 11; also monitor avian response to pond restoration and 

enhanced nesting areas and any changes in wildlife community response within 

adjacent ponds and levees)

• Continue public involvement process

• Phase 2 Work - Initiate studies in the eastern ponds in preparation for Phase 

2 restoration planning that would begin in Year 6

Years 5 and 6 – Monitoring/Adaptive Management/Lessons Learned

• Continue to implement nesting habitat enhancements within existing ponds

• Continue monitoring Pond 11 per the monitoring plan

 

• Provide an opportunity for public review of monitoring results through 

Planning Updates, public workshops, or other appropriate methods

• Phase 2 Work - Continue studies related to restoration of the eastern ponds 

Year 7 – Prepare for and Restore Ponds 10 and 10A

• Reconfigure the bay water intake system for the salt operation to allow 

continued salt production on the east side of the Otay River channel

• Review monitoring results obtained for Pond 11 and based on an evaluation of 

these results determine if any changes in restoration management, 

implementation, or design are necessary or desirable to achieve habitat goals 

and objectives
Appendix D ──────────────────────────────────────────────

 D-6 San Diego Bay National Wildlife Refuge ───────────────────────────────

• Prepare Ponds 10 and 10A for tidal restoration in accordance with final 

restoration plans (this may involve excavation or filling to achieve desired 

elevations and/or the construction of a low berm along the eastern edge of 

Pond 10A)

• Restore tidal influence to Ponds 10 and 10A

• Initiate monitoring in Ponds 10 and 10A per the monitoring plan

• Continue monitoring Pond 11 per the monitoring plan

• Continue public involvement process

• Phase 2 Work - Continue studies associated with the restoration of the eastern 

ponds and begin detailed analysis of managed pond strategies and designs 

(including brine management ponds and associated discharge requirements)

Years 8 and 9 – Monitoring/Adaptive Management/Lessons Learned

• Continue monitoring Pond 10, 10A, and 11 per the monitoring plan 

• Provide an opportunity for public review of monitoring results through 

Planning Updates, public workshops, or other appropriate methods

• Phase 2 Work – Complete studies associated with the restoration of the eastern 

ponds, prepare final engineering/restoration plans incorporating lessons 

learned from the restoration of the eastern ponds, complete environmental 

compliance documents, coordinate with appropriate agencies, and submit and 

obtain all required permit applications 

Phase 2 - Implement Restoration of the Ponds to the East of the Otay River and 

Continue to Implement Nesting Enhancement Projects throughout the Salt 

Works

Years 1, 2, and 3 – Studies, Final Restoration Planning, and Permitting for Phase 1

Year 4 – Initiate Studies for Restoration and Management of the Eastern Ponds 

• Prepare a work plan outlining the various tasks (e.g., baseline studies, prerestoration eelgrass surveys, numeric modeling, detailed analysis of the brine 

management component) needed to prepare detailed restoration plans for 

some ponds and water management plans for other ponds

• Initiate various studies and analyses per the work plan

• Explore and promote scientific research opportunities with various 

universities, USGS, and others for Phase 2 restoration activities
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-7

Years 5 and 6 – Continue Studies and Modeling of Pond Restoration and 

Management 

• Continue implementation of the work plan, including analysis of how best to 

handle gypsum and crystallized salt deposits within some of the secondary and 

pickling ponds

• Conduct detailed analyses of managed pond strategies and designs (including 

brine management ponds and associated discharge requirements) and prepare 

a water management plan to establish the operating, maintenance, and 

monitoring activities and associated costs require maintain the propose 

managed water systems

Year 7 – Prepare Final Engineering/Restoration Plans 

• Complete the tasks outlined in the work plan

• Prepare final engineering/restoration plans incorporating lessons learned from 

the restoration of Ponds 10, 10A, and 11

• Design a monitoring plan

• Continue public involvement process

• Complete environmental compliance documents, coordinate with appropriate 

agencies, and submit all required permit applications 

Years 8 and 9 – Conduct Studies and Modeling for Restoration and Management of 

the Eastern Ponds 

• Explore and promote scientific research opportunities with various 

universities, USGS, and others for Phase 2 restoration activities

• Obtain all permits required to restore tidal influence in some eastern ponds 

and manage water in other ponds

• In Year 9, prepare for removal of Ponds 12, 14, and 15 from the commercial 

salt production system

• By December 31, 2016, begin closure of the salt operation by closing the intake 

gate and continuing to move the remaining water through the system to 

produce the last harvest of salt 

Year 10 – Implement Restoration of Remaining Primary Ponds

• Prepare Ponds 12, 13, 14, and 15 for tidal restoration in accordance with final 

engineering/restoration plans

• Restore tidal influence to Ponds 12, 13, 14, and 15

• Initiate monitoring, including ground nesting seabird response to pond 

restoration and post restoration monitoring of adjacent eelgrass beds
Appendix D ──────────────────────────────────────────────

 D-8 San Diego Bay National Wildlife Refuge ───────────────────────────────

• Continue to implement nesting habitat enhancements per the restoration plans

Years 11 and 12 – Monitoring/Adaptive Management/Lessons Learned

• Continue monitoring restored areas per the monitoring plan

 

• Provide an opportunity for public review of monitoring results through 

Planning Updates, public workshops, or other appropriate methods

Year 13 – Implement Restoration/Water Management Proposals for Remaining Salt 

Ponds

• South Bay Salt Works to implement the salt works closure provisions of the 

Special Use Permit

• Prepare specified ponds for tidal restoration in accordance with final 

engineering/restoration plans 

• Prepare other ponds for long-term water management, including installing any 

new hydraulic structures needed to convey water into and/or out of the 

managed water ponds

• Restore tidal influence per the restoration plans

• Begin water management operations per the restoration plans

• Implement initial intensive water management monitoring per the water 

management plan

• Initiate monitoring of the restored ponds per the restoration monitoring plan

• Complete all proposed nesting habitat enhancements

Years 14 and 15 – Monitoring/Adaptive Management/Lessons Learned

• Continue monitoring restored and managed water areas per the appropriate 

monitoring plans

• Provide an opportunity for public review of monitoring results through 

Planning Updates, public workshops, or other appropriate methods

Monitoring

Monitoring the effects of management actions on the Refuge’s trust resources is an 

important component of the CCP, as is the documentation of the Refuge’s baseline 

conditions. By completing baseline inventories and monitoring specific management 

actions, Refuge staff can better understand the species, habitats, and physical processes 

that occur on the Refuge and the ecological interactions that occur between species. 

Monitoring is an ongoing management activity at both the Sweetwater Marsh and South 

San Diego Bay Units and will continue per available funding. Past monitoring efforts have 

focused primarily on California least tern and western snowy plover nesting, although 

monitoring of other colonial nesting birds, including the gull-billed tern, is also 

implemented at the South San Diego Bay Unit. Current monitoring efforts are adequate 
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-9

to identify trends in abundance, diversity, and nesting success of breeding seabirds and 

nesting attempts and success of snowy plovers. Monitoring programs, such as the current 

efforts, are focused on selected components that are representative of many other species 

or habitats due to funding limitations. 

Monitoring is identified as a strategy in the CCP for managing the marsh complex on the 

Sweetwater Marsh Unit and as an integral component of salt pond restoration on the 

South San Diego Bay Unit. Monitoring will focus on measuring the success of CCP 

implementation, particularly the effectiveness of the various habitat enhancement and 

restoration strategies in achieving plan objectives. The objectives provided for each 

Refuge Unit are presented in Sections 2.2.5 and 2.3.5 of Chapter 2. 

The monitoring activities associated with restoration of the Otay River floodplain and the 

salt ponds in the South San Diego Bay Unit are briefly described in Chapter 2. The 

potential salt pond restoration phasing plan, presented above, also demonstrates how 

monitoring could be incorporated into future detailed restoration plans. The specific

details of such a plan would however be defined during step-down planning. Monitoring 

activities could include, examining the establishment of vegetation and invertebrates 

during the initial phases of tidal restoration within the ponds; monitoring seabird nesting 

activity on the salt pond levees following pond restoration, and initial monitoring of the 

managed pond areas to ensure appropriate salinity levels are maintained. The data 

obtained during such monitoring will provide information necessary to confirm that the 

objectives of the various management actions are being achieved or that changes through 

adaptive management are necessary to achieve desired habitat objectives. 

Adaptive Management

Adaptive management involves sequential decision making, integrating project design, 

management, and monitoring to systematically test assumptions. Based on the data and 

lessons learned, subsequent phases of an ongoing restoration project or a new restoration 

project with similar objectives can be revised as necessary to maximize project objectives 

over time. Adequate baseline data, clearly defined and measurable project objectives, a 

monitoring plan focused on measurable results, and a process for refining and improving 

current and future management actions are all essential components of a successful 

adaptive management approach to restoration. Each of these components would be 

addressed during step down planning, and the details of the adaptive management

approach would be integrated into final restoration plans. The step-down plans will also 

describe how coordination with other science-management teams involved in implementing 

and monitoring restoration of solar salt ponds, including those involved in salt pond 

restoration in San Francisco Bay, would be achieved. 

D. Public Use

Various projects are included in the CCP that are intended to provide opportunities for increasing 

public awareness of the significance of the habitats and species protected within the Refuge, while 

also providing different ways for the public to experience these resources. The CCP emphasizes 

the importance of expanding opportunities for wildlife observation and environmental 

interpretation on both Refuge Units. In addition, the outstanding environmental education 

programs that are already being implemented on both Refuge Units would continue per available 

funding. Partners will be sought to expand the availability of these programs to more children 

throughout the region, while also expanding the depth of the programs to address the needs of 
Appendix D ──────────────────────────────────────────────

 D-10 San Diego Bay National Wildlife Refuge ───────────────────────────────

older students. Other opportunities for public outreach would also be realized by continuing to 

permit fishing and boating within the South San Diego Bay Unit. 

E. Step-Down Plans

Some projects such as public use programs and habitat restoration proposals require more indepth planning than the CCP process is designed to provide. For these projects, the Service 

prepares step-down plans. Step-down plans provide additional planning and design details 

necessary to implement the strategies (projects or programs) identified in the CCP. Two stepdown plans – the Fire Management Plan and Predator Management Plan – are included in this 

CCP as Appendices L and M, respectively. Several step-down plans are proposed for completion 

following the approval of the CCP including a Habitat Management Plan and an Interpretive Trail 

Plan for the Sweetwater Marsh Unit and detailed restoration planning for the South San Diego 

Bay Unit. 

F. Compliance Requirements for Plan Implementation

All projects and step-down plans described in the CCP will be required to comply with NEPA and 

the Improvement Act, as well as a variety of other Federal regulations, executive orders, and 

legislative acts, which are described in greater detail in Chapter 5 of this document. The Final EIS 

is intended to address all proposed actions at the program level; however, some actions once 

defined in greater detail may require additional analysis and review under NEPA. In addition, all 

projects that involve disturbance of the land, changes to structures more than 50 years old, and/or 

changes to the use, design, and/or function of the salt works, which has been deemed eligible for 

inclusion on NRHP, would require coordination with the Regional Archaeologist. To initiate 

review by the Regional Archaeologist, a Request for Cultural Resource Compliance would be 

prepared early in the planning process for each proposed project. 

G. Anticipated Costs of Fully Implementing the CCP

Funding for Projects

The estimated costs for the various projects described for the preferred alternatives, as well as 

the new staffing requirements for implementing these projects, are presented in Table D-3. 

The costs presented under the heading Recurring Base include the anticipated long-term 

annual costs of maintaining equipment, structures, facilities, signage, and/or restored or 

enhanced habitat areas, as well as the annual costs of maintaining programs such as existing 

and proposed environmental education, interpretation, and volunteer programs. 

Current and Future Staffing

To implement all of the proposed actions and achieve the goals and objectives of the CCP for 

the two Refuge Units, additional funding and staff will be necessary. Tables D-4 and D-5 

present the current and future (proposed) funding and staff needs for the combined 

management of the Sweetwater Marsh and South San Diego Bay Units. The base budget in 

FY2004 for the three San Diego Coastal Refuges: Sweetwater Marsh Unit, South San Diego 

Bay Unit, and Tijuana Slough NWR was $802,000. 

Table D-5 presents the proposed future staffing requirements for the San Diego Coastal 

Refuges based on the types of projects that are proposed within the CCP. 
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-11

Table D-3 

ESTIMATED COSTS FOR IMPLEMENTING CCP PROJECTS 

AND PROPOSED STAFFING INCREASES TO IMPLEMENT AND MAINTAIN THESE 

Projects Proposed to Achieve Refuge Goals and Objectives Operating C

FTEs OneTime 

Habitat and Wildlife ManagementIncrease habitat management activities within the Sweetwater Marsh Unit: 

Develop and implement a Habitat Management Plan that includes actions to improve and protect 

marsh quality including completion of an inventory of marsh species and mapping of special status species distribution/population size; improving conditions in upland transition areas to benefit salt marsh bird’s beak propagation; increasing control of invasive plants; and performing annual monitoring and maintenance activities. 

- $25 

Enhance and maintain tern and plover nesting habitat and improve nesting success: 

Enhance existing nesting areas at the D Street Fill and on the salt pond levees by adding a 6- to 8-inch 

layer of clean, light-color sand to areas with poor substrate quality, and by improving chick access to adjacent foraging areas. Follow up annually with 1) preseason tern and plover nest site preparation to control vegetation and maintain quality nesting substrate; 2) predator management to minimize losses of least tern and snowy plover eggs, chicks, and adults to avian and mammalian predators during the nesting season, and 3) monitoring site use by nesting least terns and snowy plovers and recording the reproductive success of each species within the two nesting areas. 

- $75 

Improve nesting habitat for plovers within the salt pond complex: 

Seasonally manage the water level in Pond 20 or other appropriate pond to provide a minimum of 20 

acres of dry salt flats in proximity to quality foraging areas to support western snowy plover nesting. 

- $5 

General Refuge Management Reduce unauthorized access onto the Refuge: 

Develop and implement a public outreach program directed at reducing unauthorized access by people 

and their pets into sensitive Refuge habitats. The program, which should be design and implemented in partnership with other agencies and organizations, should incorporate the use of effective signage, brochures, and a speakers bureau (traveling public information program) to inform the public of the need to protect the sensitive resources on the Refuge; expand law enforcement and Refuge staff 

visibility on the Refuge, and encourage stewardship through hands-on volunteer opportunities. 

- $15 
Appendix D ──────────────────────────────────────────────

 D-12 San Diego Bay National Wildlife Refuge ───────────────────────────────

FTEs OneTime 

General Refuge Management (cont.)Reduce disturbance to wildlife in the open waters of the Refuge: Coordinate with the Coast Guard and Harbor Patrol to ensure enforcement of the designated 5 mph speed limit throughout the south bay and acquire a patrol boat to increase Refuge law enforcement presence within those portions of the Refuge located within San Diego Bay.

- $50 

Secure the eastern perimeter of the salt pond complex following closure of the salt operation: 

Install and maintain appropriate fencing and signage around the eastern perimeter of the salt ponds to minimize the incidence of unauthorized access into the area and to discourage entry into the area by stray dogs, cats, and other mammals that could pose a threat to nesting and feeding wildlife. 

- $45 

Reduce the accumulation of fishing line within the Refuge: Develop and implement a Monofilament Recovery & Recycling Program to raise awareness about the 

dangers to wildlife of improperly discarding fishing line. 

- $15 

Prepare a Cultural Resource Management Plan for the Refuge: 

Identify, record, and evaluate the cultural resources on the Refuge. With this information, develop 

and implement a cultural resource management plan, in consultation with all interested parties, that insures the long-term protection of the Refuge’s sensitive cultural resources and encourages the 

interpretation of these resources as part of the overall interpretive program for the Refuge. 

- $25 

Address contaminants issues affecting the Refuge: Develop and implement baseline sampling plans for potentially contaminated areas within the Refuge. 

Seek additional funding to develop and implement remediation plans for those areas that are 

determined to require remediation due to existing contaminant levels.

- $100 

Improve volunteer services within the Refuge: 

Design a volunteer program for the San Diego Bay NWR that when implemented will improve and 

expand volunteer opportunities within the Refuge. Obtain basic supplies, equipment, and uniforms for 

the volunteers and design and implement a volunteer program that would support existing and 

expanded proposals for environmental education, interpretation and wildlife observation, assist Refuge staff in accomplishing projects related to habitat and wildlife management (e.g., wildlife and plant surveys, invasive species control, native plant propagation and planting, construction of nesting platforms), and facilitate other special events.

- $25 

Public UseRedesign the existing trail system and interpretive signage on Gunpowder Point: 

Design and implement an environmental interpretation plan for Gunpowder Point that includes a 

redesigned trail system and new interpretive signage to improve opportunities for wildlife observation, as well as to compliment and support the Refuge’s existing environmental education programs. 

- $150 
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-13

FTEs OneTime 

Public Use (cont.) Increase participation in existing environmental education programs:

Continue to assist in the funding and implementation of the Refuge’s environmental education 

program, particularly the Habitat Heroes and Sweetwater Safari Programs, with the goal of renewing

existing partnerships and identifying new partners to assist in expanding current outreach programs 

to better serve underrepresented and underserved communities. 

- $15 

Increase opportunities for guided tours of the salt ponds: Expand the number of guided tours provided at the salt works and acquire an electric multi-passenger 

vehicle to transport visitors along the levees. 

- $60 

Develop a pedestrian pathway along the southern edge of the Refuge: 

Design and construct a pedestrian pathway from 7th to 10th Street, north of the Bayshore Bikeway, to 

provide opportunities for wildlife observation, environmental education, and interpretation. 

- $650 

Develop an interpretive overlook at the end of 10th Street: 

Partner with the City of Imperial Beach to improve access to and develop an interpretive overlook on the coastal terrace just to the north of the Bayshore Bikeway and install interpretive panels and spotting scopes to provide opportunities to observe the birds that nest, forage, and rest within the restored salt ponds. 

- $50 

Construct an observation area at the end of 8th Street: 

Design and construct an observation area to the north of the Bayshore Bikeway at the end of 8th Street 

in Imperial Beach to expand opportunities for wildlife observation and interpretation. 

- $25 

Improve wildlife observation opportunities at the east end of the Refuge: Design and construct an observation area at the edge of Pond 29. - $20 Develop an Interpretive Nature Trail Around Pond 28:

Design and construct an accessible, 1.5-mile interpretive nature trail around Pond 28 following the 

closure of the salt works. 

- $450 

Design and implement an interpretive program about the history of hunting in San Diego Bay:

Working with partners representing the hunting community, design and implement an interpretive program that would be conducted along the outer levee of the eastern salt ponds in late fall to interpret waterfowl hunting, historic hunting on the south bay, and hunting within the National Wildlife Refuge System. 

- $5 

Habitat Restoration and EnhancementEnhance water circulation in Sweetwater Marsh/Paradise Marsh: 

Remove old fill areas, construct a new culvert, and remove/lower a weir to enhance tidal circulation 

over 130 acres of marsh habitat to benefit listed species and migratory birds. 

- $250 
Appendix D ──────────────────────────────────────────────

 D-14 San Diego Bay National Wildlife Refuge ───────────────────────────────

FTEs OneTime 

Habitat Restoration and Enhancement (cont.)Restore intertidal wetlands on the Sweetwater Marsh Unit: 

After 2010, when the existing mitigation leasehold overlays expire, restore up to 20 acres of intertidal wetlands, of which a minimum of ten acres would be restored to cordgrass-dominated salt marsh habitat. The actual areas available for restoration would be dependent upon how much restoration is implemented on the mitigation leasehold overlays prior to 2010. Potential restoration areas include approximately 13 acres at the eastern end of the D Street Fill, six acres at the F&G Street Marsh, and two acres along the northern edge of Gunpowder Point. 

- $2,000 

Restore native upland and upland transition habitat on the Sweetwater Marsh Unit: After 2010, when the existing mitigation leasehold overlays expire, restore approximately 25 acres on Gunpowder Point to native upland vegetation and restore the native plant species historically found in the wetland-upland transition areas throughout the Refuge Unit. This project would involve the initial removal and long-term control of invasive, non-native species, planting and seeding of native vegetation, initial monitoring of restoration success, and long-term maintenance and monitoring of the restored habitat. 

- $300 

Improve tidal circulation at the southern tip of Sweetwater Marsh: Conduct a hydrologic study to analyze the benefits of removing the berm located between the bay and the southern tip of Sweetwater Marsh, and if benefits to tidal circulation and habitat quality would be 

realized, prepare and implement engineering plans for removing or breaching the berm. 

- $750 

Increase the total acreage of nesting habitat within the salt pond complex: 

Create a minimum of 33-acres of new nesting habitat within the salt pond complex by filling pond corners, creating “island” type fills within the ponds, widening some levees, recontouring some levee side slopes, and capping all nesting areas with appropriate depths of clean, light sand to benefit the California least tern, western snowy plover, and other ground nesting birds that nest on the levees.

- $2,500 

Restore native wetland and upland habitat in the Otay River floodplain: Develop and implement step-down restoration plans to restore approximately 145 acres of disturbed 

habitat in the Otay River floodplain, creating freshwater wetland, coastal salt marsh, and native scrub habitats to benefit endangered species, migratory birds, and other Refuge resources. 

- $5,000 

Restore the western salt ponds to tidal action: In accordance with final restoration plans and the associated phasing plan, prepare the western ponds 

for intertidal restoration and then breach the pond levees to restore 200 acres of intertidal habitat. 

- $2,000 

Restore the eastern primary salt ponds to tidal action: In accordance with final restoration plans and the associated phasing plan, prepare the eastern ponds 

for tidal restoration, then breach the pond levees to restore 240 acres of salt ponds to tidal influence. 

- $1,500 
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-15

FTEs OneTime 

Habitat Restoration and Enhancement (cont.)Convert the remaining salt ponds to tidal marsh and managed water areas: Restore an additional 200 acres of secondary salt ponds to tidal influence and implement measures to 

manage salinity, water levels, and water flow within the remaining 275 acres of salt ponds. 

- $1,500 

Additional Staff/Contracting Needs to Achieve Refuge Goals and Objectives Implement a predator management program to protect listed species:

Contract with APHIS-WS or other comparable contractor to conduct avian and mammalian predator 

control on the Refuge to protect listed species. Predator control would be implemented in accordance with the Refuge’s approved Predator Management Plan. 

1 - 

Provide oversight of all Refuge operations and maintenance and management activities:

Hire a Refuge Operations Specialist to work directly with the Refuge Manager to provide oversight of 

general Refuge operations and programs, including maintenance, visitor services and outreach, volunteer activities, and the Youth Conservation Corps.

1 _$2 

Maintain and manage the Refuge’s natural and managed habitat areas and other facilities:

Hire a Maintenance Worker/Heavy Engineering Equipment Operator to maintain the levees within 

the restored salt pond complex; install and maintain fencing and signage around the Refuge, where needed; annually conduct preseason nest site preparation on the D Street Fill and the salt pond levees; maintain and repair water structures, pumps, or other equipment needed to manage water in some of the salt ponds; and conduct other duties as necessary to maintain Refuge habitats and facilities. 

1 $50 

Implement the Refuge’s various habitat management and monitoring plans:

Hire a Biological Technician to assist the Wildlife Biologist in developing and implementing a Habitat 

Management Plan for the Sweetwater Marsh Unit and a future monitoring and maintenance plan for the restored salt ponds that include actions to improve and protect marsh quality (e.g., completion of an inventory of marsh species and mapping of special status species distribution/population size; improving conditions in upland transition areas on the Sweetwater Marsh Unit to benefit salt marsh bird’s beak propagation; increasing control of invasive plants; performing annual monitoring).

1 $5 

Improve volunteer services on the Refuge:

Hire a volunteer coordinator to develop and implement a volunteer program that will support wildlife 

and habitat management (e.g., monitoring activity in least tern and snowy plover nesting colonies,

assisting with revegetation programs) and visitor services (e.g., docent programs, nature guides).

.6 $5 

Provide oversight of wildlife and habitat management programs:

Hire a Supervising Wildlife Biologist to oversee all projects related to wildlife and habitat 

management, habitat restoration and enhancement, and listed species recovery on the Refuge.

.6 $5 
Appendix D ──────────────────────────────────────────────

 D-16 San Diego Bay National Wildlife Refuge ───────────────────────────────

Table D-4 

Current Staffing Positions for the San Diego Coastal Refuges 

Staff Type Employment Status FTE Salary Rating 

Management

Project Leader PFT 0.6 GS 14 

Deputy Project Leader PFT 0.6 GS 13 

Refuge Manager PFT 1 GS 12 

Refuge Operations 

Specialist 

PFT 1 GS 11 

Administrative 

Administrative Assistant PFT 0.6 GS 7 

Biology 

Wildlife Biologist PFT 1 GS 11 

Public Use 

Park Ranger PFT 1 GS 5

Refuge Officer PFT 1.5 GS 7/9 

Information and 

Education Specialist 

PFT 0.6 GS 11 

Instructional Systems 

Specialist

PFT 0.6 GS 9

Refuge Planner PFT 0.6 GS 12 

Table D-5

Future (Proposed) Staffing for the San Diego Coastal Refuges 

Staff Type Employment Status FTE Salary Rating 

Management

Project Leader PFT 0.6 GS 14 

Deputy Project Leader PFT 0.6 GS 13 

Refuge Manager PFT 1 GS 12 

Refuge Operations 

Specialist 

PFT 2 GS 11 

Administrative 

Administrative Assistant PFT 0.6 GS 9

Receptionist/ 

Clerk/Typist 

PFT 0.6 GS 6 

Biology 

Supervising Wildlife 

Biologist 

PFT 0.6 GS 12 

Wildlife Biologist PFT 1 GS 9 

Biology Technician PFT 1 GS 7 
────────────────────────────────────────────── Appendix D

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement D-17

Table D-5 (continued) 

Public Use 

Park Ranger PFT 1 GS 5

Volunteer Coordinator PFT 0.6 GS 7 

Information and 

Education Specialist 

PFT 0.6 GS 11 

Instructional Systems 

Specialist

PFT 0.6 GS 9

Refuge Planner PFT 0.6 GS 12 

Refuge Officer PFT 1.5 GS 9 

Maintenance 

Maintenance 

Worker/Heavy 

Engineering Equipment 

Operator 

PFT 0.6 WG 8 

Land Acquisition

The Service will continue to negotiate with the Port, City of Chula Vista, and State Lands 

Commission to secure management authority for all open water areas included within the 

approved acquisition boundary for the South San Diego Bay Unit. 

H. Potential Funding Sources for Implementing CCP Projects 

Several projects included in the CCP may be implemented in full or in part by sources other than 

the Refuge annual budget. These projects, which could include enhancement and restoration 

projects and public use-related projects, could be funded through partnerships with other local, 

state, or federal agencies, special legislative appropriations, or grants (i.e., Friends of the San 

Diego Refuges, National Fish and Wildlife Foundation, Ducks Unlimited, San Diego Audubon, 

Transportation Enhancement Funds). Other potential sources of funding for restoration projects 

include: the North American Wetlands Conservation Act Grants Program; the California Coastal 

Conservancy’s Southern California Wetlands Recovery Project; the Service’s National Coastal 

Wetlands Conservation Grant Program, if implemented in partnership with the State of California; 

the Cooperative Endangered Species Conservation Fund, also if implemented in partnership with 

the State of California; NOAA’s Damage Assessment and Restoration Program for restoration 

projects applicable to specific oil spills or hazardous substance releases such as the American 

Trader Oilspill; restoration projects applicable to contaminants restoration programs (i.e., 

Montrose Settlements Restoration Program); and partnerships with the U.S. Army Corps of 

Engineers (Corps) under Sections 704, 906(b), and/or 1135 of the Water Resources Development 

Act of 1986. The Estuary Restoration Act of 2000 also authorizes a program under which the 

Corps can carry out restoration projects when the costs of the project are shared with non-Federal 

parties, however, funds to implement these types of programs have not yet been appropriated. 

I. Partnership Opportunities

Long before the establishment of these Refuge Units, there was strong public interest in the 

protection, management, and stewardship of the habitats now preserved within the Refuge. This 

interest has continued, and several programs on the Refuge both existing and planned are made 

possible through a variety of public/private and interagency partnerships. Some of these 

partnerships focus on providing regionally significant environmental education programs (e.g., 

Sweetwater Safari and Habitat Heroes), while others focus on expanding opportunities for public 
Appendix D ──────────────────────────────────────────────

 D-18 San Diego Bay National Wildlife Refuge ───────────────────────────────

use and improving habitat quality for fish and wildlife (e.g., clean ups sponsored by the Port, the 

Friends of the San Diego Refuges, and the Audubon Society, guided tours conducted by the Chula 

Vista Nature Center). The proximity of the Refuge to urban development and the international 

border with Mexico, along with the designation of the Refuge as globally significant habitat, has 

and will continue to result in the development of unique and innovative partnerships with the local 

community and local, state, national, and international agencies and organizations. 

Existing partnerships such as those between the Service and the Chula Vista Nature Center, San 

Diego Zoological Society, SeaWorld, SWIA, and many others will be strengthened and new 

partnerships will continue to be nurtured. New and existing partnerships will expand community 

support for the Refuge, increase stewardship of Refuge resources, and provide greater benefits to 

wildlife resources and the public than would be achievable within the Refuge’s annual budgets. 

Partnerships will be particularly important in obtaining funding to implement proposed habitat 

enhancement and restoration projects. More details regarding these types of partnerships are 

presented under the project funding and staffing discussion.
 

Appendix E 

Summary of Public Scoping Comments 
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement E-1

Appendix E: Summary of Public Scoping 

Comments 

Introduction

The scoping process for the San Diego Bay NWR CCP is described in detail in Section 5.2 of the 

Final CCP/EIS. Comments related to the CCP were received via mail, email, and verbally at the 

initial scoping meetings. Additional comments were provided throughout the planning process, 

particularly during and immediately following the various public workshops held to address 

specific issues related to the CCP. A summary of the scoping comments is present below by topic. 

Summary of Scoping Comments

ACQUISITION/BOUNDARY ISSUES 

• Initiate the procedures necessary to take control (acquire/protect) of all lands and waters 

within the acquisitions boundaries for the South San Diego Bay Unit. 

• Include all of the tidal mudflats in South San Diego Bay into the refuge boundaries, 

including the mudflats at Emory Cove, in the vicinity of the J Street Marina, and along 

Sweetwater Marsh. 

• Extend the acquisition boundary for the South San Diego Bay Unit to the boundary for the 

Sweetwater Marsh Unit to create one continuous refuge. 

• Incorporate into the Sweetwater Marsh Unit those portions of the D Street fill that are 

located to the north and west of the current refuge boundaries. 

• Include all of Pond 20A within the South San Diego Bay Unit. 

PUBLIC USE 

General 

• Emphasize the wildlife first perspective when considering the type and intensity of public 

uses to be permitted uses should not be permitted that would negatively impact 

endangered or other species. 

• Limit public use because the refuge has been established for nesting birds. 

• Link the public uses on the refuges to other public use areas, such as the Otay Valley River 

Park. 

• Management goals should emphasize wildlife/habitat protection over public recreation 

uses. 

• Promote ecotourism with minimal impacts to resources. 

• Withhold final compatibility determination until population information is presented and 

analyzed. 

• Include in the CCP, a thorough evaluation of all recreational activities presently allowed on 

the refuges and their impacts on native flora and fauna, especially threatened and 

endangered species. 

• Maintain compatible wildlife-dependent recreational activities as a major component of the 

programs of the refuges. 

• Strike a balance between wildlife and people, and manage the refuge as a place for people 

as well as wildlife, by accommodating passive, quiet human use. 

• Manage public use to ensure that the refuge is maintained as a quiet place for waterfowl – 

the San Diego Bay is heavily used in almost all other areas, even kayaks in small numbers 

could have an impact on waterfowl. 
Appendix E ──────────────────────────────────────────────

E-2 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

• Don’t restrict access to the refuges; rather take this as an opportunity to build support 

from future generations. 

Hunting/Fishing 

• Provide opportunities for dog trials and retrieval training. 

• Prohibit dogs on the refuge. 

• Provide opportunities for hunting. 

• Prohibit consumptive use of wildlife on the refuge. 

• Provide opportunities for fishing. 

• There are enough fishing opportunities elsewhere in San Diego. 

• Provide for youth-related hunting and fishing experiences. 

• Prohibit hunting on the refuge. 

Wildlife Observation

• Provide visual access to the bird colonies on the Salt Works through the use of video 

cameras. 

• Provide access on the levees for viewing migratory birds within the Salt Works. 

• Provide elevated bird blinds at the edges of the Salt Works to provide views of the 

migratory birds. 

• Integrate bird viewing areas along the proposed Bayshore Bikeway. 

• Consider the installation of elevated viewing platforms for wildlife viewing between 11th

and 12th Streets next to the bike path and north of the Salt Works in the industrial area. 

• Preserve the existing sound (ambient noise) characteristics of the salt ponds – avoid 

increasing human generated sounds in order to preserve evening silence, existing bird 

“chatter”, and other nature sounds of this environment. 

Wildlife Photography 

• Provide bird blinds specifically for photographers. 

• Provide for tourist photo opportunities. 

Environmental Education 

• Encourage more involvement with schools (K-6). 

• Promote education by providing access for kids. 

• Provide education/interpretive programs at the South Bay Unit and Paradise Marsh. 

• Select places to education the public about these coastal resources that will not result in 

impacts in birds in the area. 

• Educate the public about endangered species and how their survival is linked to human 

survival. 

• Provide educational opportunities/birding brochures in Spanish. 

• Working with partners, such as the City of National City and Paradise Creek Educational 

Park Inc., develop interpretive park elements in Paradise Marsh. 

• Explain in the CCP how environmental education and interpretation will be provided and 

identify how these programs will relate to and support the purpose of the refuges. 

Environmental Interpretation 

• Provide duck feeding stations. 

• Consider South Grand Caribe Island as a place for an interpretive stop on a kayak trail. 

• Develop a comprehensive (e.g., biological resources, history, agriculture, culture, industry) 

and coordinated interpretive signage program around San Diego Bay. 
Appendix E ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement E-3

• Create a multi-agency brochure that illustrates where all the interpretive signage around 

the bay are located. 

• Establish a satellite interpretive facility near Bay View Elementary School. 

• Provide interpretive areas/features through the refuge areas. 

Boating 

• Provide kayaking opportunities in the South Bay, including interpretive trails, resting 

areas and rentals. 

• Provide a viewpoint for boaters, such as an island. 

• Establish restrictions for boats and aircraft, including ultra-lights. 

Trails 

• Provide seasonal walking/jogging/birding trail around Ponds 10 and 11. 

• Prohibit public access within the salt works. 

• Limit public access to those areas in which such use would be compatible with wildlife 

resources, since inappropriate public access could result in impacts to threatened and 

endangered species, as well as all other nesting birds. 

• Provide for a walking path adjacent to the Bayshore Bikeway. 

• Allow bicycles to ride to Gunpowder Point on the Sweetwater Marsh Unit. 

• Reduce motorized activity through Sweetwater Marsh. 

• Consider the installation of boardwalks south of the J Street Marina over the existing 

mudflats and near the county park on the west side of the bay. 

• Limit access to designated trails only and consider the use of physical barriers to ensure 

that trail users stay on the trail. 

• Allow seasonal use of the dikes for walking. 

Research 

• Identify research opportunities that the refuge can support without adversely impacting 

biological resources or wildlife-dependent recreation. 

WILDLIFE/HABITAT MANAGEMENT 

General 

• Develop management goals that are science-based and reflect the principles of 

conservation biology. 

• Conduct a rigorous biological assessment and inventory of all flora and fauna inhabiting 

the refuge. 

• Prior to planning, complete a thorough discussion and investigation of the biological 

integrity, diversity, and environmental health of the refuge areas. 

• Follow the standardized sequence for refuge planning suggested in “Science-Based 

Stewardship: Recommendations for Implementing the National Wildlife Refuge System 

Improvement Act” (biological inventory ⇒ identification of plan goals ⇒ identification of 

threats ⇒ choice of focal species ⇒ CCP ⇒ monitoring and implementation ⇒ plan 

amendment [according to monitoring results]). 

• Protect and, where appropriate, enhance wildlife habitat. 

• Prepare monitoring and management procedures, define species habitat and monitoring 

protocols consistent with the MSCP protocols; conduct data management and reporting to 

allow integration with other MSCP preserve areas. 

• Identify potential stressors of the lower Otay River and Sweetwater River systems. 

• Ensure that conservation efforts/management do not degrade existing suitable habitat. 

• Avoid developing a CCP that is a “mitigation dump.” 
Appendix E ──────────────────────────────────────────────

E-4 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

• Reintroduce extirpated species. 

• Incorporate adaptive management into the CCP through management goals, objectives, 

and strategies. 

• Create corridors to connect different areas of the refuge. 

• Avoid Habitat Evaluation Process (HEP) analysis. 

• Preserve/enhance brackish marsh/freshwater habitat interface. 

• Develop and maintain a database of pertinent scientific information regarding habitats and 

wildlife. 

• Discuss in the CCP how anticipated trends in human population density and recreational 

use and other significant trends or anticipated problems will affect the distribution and 

abundance of native plants and animals on the refuges. 

Predator Control 

• Provide aggressive predator control for the protection of threatened and endangered 

species and other nesting species. 

• Eliminate domestic and feral cats from the refuge year round. 

• Make the dikes at the salt works predator proof. 

• Use effective, long-term management strategies for protecting threatened and endangered 

species that are both humane and socially acceptable. 

• Include a thorough discussion of predator control in the CCP. 

• Incorporate into the predator control discussion, recent scientific research regarding nonlethal predator management methods for protection of threatened and endangered species, 

specifically with regard to predator exclusion techniques. 

Consideration of Specific Organisms

• Consider the effects of restoration proposal on all species, not just endangered species (i.e. 

shorebirds versus least tern). 

• Maintain/enhance existing habitat values for all currently occurring native species 

(shorebirds, nesting habitat for terns and shorebirds). 

• Restore waterfowl habitat to original conditions, provide habitat for brants and widgeons. 

• Create salt marsh that provides functional habitat for Belding’s savannah sparrows, 

clapper rails, etc. 

• Include specific management strategies for sea turtles. 

• Consider insects, including wandering skipper, salt marsh skipper, globos dune beetle, 

tiger beetle, and lutica sand spiders, in protection, enhancement, and restoration planning. 

• Study invertebrate populations in all habitats, terrestrial and aquatic. 

• Restore the population of silvery legless lizards in the dunes. 

• Pursue rare plant restoration and enhancement for species such as Dudleya variegata and 

Lotus nuttlaliauus. 

• Establish as the primary management goal actions that benefit wintering and breeding 

birds. 

• Optimize habitat conditions during the winter as well as during breeding season. 

• Maximize nesting sites for terns, skimmers, and plovers. 

• Manage the refuge primarily for the protection of migratory birds, breeding, and wintering 

birds. 

Salt Ponds 

• Consider the existing benefits of the salt works for shorebird use. 

• Preserve brine shrimp, brine fly, hypersaline habitat to provide food source. 

• Restore marsh habitat in the salt ponds without destroying the hypersaline habitat. 
Appendix E ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement E-5

• Maintain the current salt works to preserve the current hypersaline environment. 

• Restore the habitat in the salt ponds. 

• Develop an understanding of the salt works ecosystem and its benefit before implementing 

changes. 

• Explore if and how brine shrimp could be maintained in the salt ponds without making salt. 

• Understand the different target areas of habitat enhancement/restoration will have 

different impacts on the integrity of salt production capacity (the more dilute the unit, the 

less effect on the system). 

• Phase any changes in the salt operation to avoid impacts to existing habitat quality – don’t 

disrupt the biogeochemistry of the system. 

• Investigate various sizes of salt works operations that would be consistent with 

management objectives. 

• Maintain the dikes within the salt ponds whether or not the salt making operation is 

continued. 

• Breach the dikes within the salt ponds to create islands, if the salt making operations are 

discontinued. 

• Consider creating nesting islands in the salt ponds. 

• Consider Pond 10A as important biological habitat for herons and egrets. 

Uplands

• Preserve upland transition areas and upland habitat around the Bay for sensitive and 

candidate species such as Loggerhead Shrike, Burrowing Owl, Northern Harrier, Horned 

Lark, and jack rabbit. 

RESTORATION 

Sweetwater Marsh Unit 

• Restore Paradise Marsh, including reworking unsuccessful or incomplete restoration 

projects. 

• Expand and reconnect the former 5.6 acres of marsh north of F Street to the F&G Street 

Marsh. Remove J Street in this area. 

• Restore and improve tidal action in the F&G Street Marsh. 

South San Diego Bay Unit 

• Restore the degraded portions of the Otay River, while protecting existing important 

shorebird foraging areas. 

• Integrate the restoration of Nestor Creek into the Otay River restoration proposals 

• Restore coastal sage scrub on Egger-Ghio. 

• Re-establish corridors between the Otay River Valley and the Bay for upland birds. 

• Restore degraded salt ponds. 

• Determine the most appropriate hydrologic restoration objectives for Egger-Ghio, and 

then develop a conceptual habitat restoration plan that is consistent with these objectives. 

• Seek to correct problems at the Chula Vista Wildlife Reserve. 

• Evaluate the extent of restoration, protection, and enhancement of habitats that is needed 

to sustain healthy populations of native plants and animals on the refuge. 

MANAGEMENT OF INVASIVE SPECIES 

• Eliminate/control non-native, invasive plants. 

• Control/eradicate populations of Argentine ants on the refuge. 

• Develop strategies for preventing new invasive species from becoming established on the 

refuges. 
Appendix E ──────────────────────────────────────────────

E-6 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

• Identify the current invasive species problems on the refuges and identify appropriate 

management responses. 

HYDROLOGY/WATER QUALITY 

• Identify methods for improving the quality of the runoff/storm water that flows from 

Nestor Creek and the Otay River, while also improving wetlands. 

• Conduct a hydrologic study of Nestor Creek to determine if there is a connection between 

South Bay and the Tijuana floodplain. 

• Evaluate the geomorphology of the lower Otay River, including its tributary canyons, to 

determine which wetland communities can be supported in the area. 

• Address measures needed to maintain or restore water quality. 

OPERATIONS 

General Issues 

• Develop a management overlay for the north end of the Otay River to give the Service 

some management authority. 

• Monitor speeds in the bay and strictly enforce the 5 mph speed limit. 

• Ensure adequate staff, training, and equipment for the refuge. 

• Establish a long-term, extensive monitoring/research program to evaluate changes on the 

refuge. 

• Monitor and record public access effects on wildlife. 

• Secure the perimeter of the Sweetwater Marsh Unit to minimize unauthorized public 

access, particularly at the Sweetwater Channel and Paradise Creek intersection. 

PROCDURAL ISSUES 

• Conduct bilingual meetings and provide bilingual handouts/meeting notices. 

• Work closely with the environmental community. 

• Involve a group of stakeholders in the planning process. 

• Allow Audubon to participate on the core team. 

• Conduct single-issue public workshops. 

• Make the vision statement and goals for the refuges available for public review and 

comment during the scoping and well before the preparation of the CCP and NEPA 

document. 

• Take care to ensure that compliance with both NEPA and the Refuge Act are 

accomplished in the combined draft CCP/environmental document. 

• Ensure that the California Department of Fish and Game is given the opportunity to 

participate in the process. 

• Establish mechanisms to provide for thorough and responsive feedback to public 

comments made during the planning process. 

PLANNING 

• Allow for green space/park on the south end of Pond 20A and Egger-Ghio. 

• Consider the inclusion of an oil spill mitigation plan in the CCP. 

• Provide graphics in the CCP that demonstrate how the coastal areas are connected to the 

inland areas. 

• Keep the planning process short and begin implementation immediately upon CCP 

approval. 

• Consider the regional planning resource conservation and management objectives for the 

lower Otay River and Sweetwater River when developing the CCP. 

• Address the relationship of the CCP to other existing landscape-level planning efforts. 
Appendix E ──────────────────────────────────────────────

───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement E-7

• Establish and clearly state priorities for the activities proposed in the plan. 

ADJACENT LAND USES

• Identify opportunities to connect commercial interests to the refuge. 

• Work to achieve a good transition between Refuge property and any future commercial 

development that occurs on the south end of Pond 20A. 

• Limit development between the two portions of Sweetwater Marsh and the adjacent bay 

front. 

• Coordinate with Chula Vista planning regarding development adjacent to Sweetwater 

Marsh. 

PARTNERSHIPS 

• Identify specific partnership opportunities for funding projects or creating volunteer 

projects. 

STEWARDSHIP PROJECT ISSUES 

• Protect the snowy plover nesting areas on the site. 

• Identify mitigation for the Navy on the Stewardship Project area – then the Stewardship 

Project could be replaced with a Refuge Overlay. 

• Restore vernal pool habitat on the site. 

• Remove Carpobrotas edulis at the site before it takes over everything on the dunes and 

other uplands. 

• Survey for fairy shrimp in the existing vernal pools. 

BAYSHORE BIKEWAY 

• Provide screening along the bikeway in locations where shorebirds using the salt pond 

areas could be flushed. 

• Select the least destructive route for the bikeway. 

• Reroute the bike path from the tracks to the berm located on the south side of the tracks to 

allow more opportunities for river restoration. 

• If Pond 20A is developed, aligned the bike path within the refuge/development interface. 

• Upgrade the existing bike path. 

• Complete the Bayshore Bikeway from E Street north to 24th Street. 

MISCELLANEOUS QUESTIONS 

• What is the timing for beginning work on the Stewardship Project? 

• Why is Pond 20A excluded from the Refuge boundary, since it is an integral part of the 

system? 

• Is the western refuge boundary provided on the maps correct? Why are the channels 

leading to the Coronado Cays not shown on the maps? What is their status with regards to 

the Refuge? Does the FWS have jurisdiction over them? Was this negotiated before the 

refuge was established? 

• Who should someone call to report unauthorized activity on the refuge? 

• Who has jurisdiction on the refuge (land/water)? 

• If the South Bay Power Plant goes off line, what constraints would be placed on restoration 

due to the presence of sea turtles in the area? 

• What is the biological status of pond 20A? 

• Is the Comprehensive Conservation Plan a regulatory document for a local jurisdiction? 

• What is the full range of alternatives that may be considered? 
Appendix E ──────────────────────────────────────────────

E-8 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

• The recognition of edge effects typically has what response from your agency, internal or 

external redress? 

• Does a Comprehensive Conservation Plan include recommendations for land use changes 

or development standard modifications on properties adjacent, upstream, or near a refuge? 

• Will hunting be considered as a possible public use on the refuge? 

• Will there be any consideration of proposing additional boating restrictions on the Bay? 
 

Appendix F 

Description of the Salt Works Operation 
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement F-1

Appendix F: Description of the Salt 

Works Operation 

Brief History 

The first formal reference to a commercial solar salt operation in south San Diego Bay is that of 

the La Punta Salt Works, which according to historic records began salt production in 1871 

(Gustafson and Gregory 2001). Salt production in the south bay may however have begun prior to 

that time, based on one record from the San Diego Division of Natural Resources that cited 300 

tons of salt production in San Diego Bay in 1870. The exact location of the La Punta Salt Works 

has not been verified, but is believed to have been located to the southwest of the current salt plant 

on Bay Boulevard. This facility appears to have been in operation until about 1901. In 1902, the 

Western Salt Company established a solar salt operation about a quarter of mile northeast of the 

La Punta Salt Works (Gustafson and Gregory 2001) within a portion of the present day salt works. 

By 1911, this operation had expanded into the south end of the bay. Additional changes to the 

configuration of the ponds have occurred since that time. The current operation encompasses 

approximately 1,035 acres and incorporates much of the southern end of San Diego Bay (Figure F1). With the exception of brief closure in 1916 when flood waters severely damaged the salt plant 

and several ponds, salt has been produced continuously at this site since 1902. 

Current Operation

South Bay Salt Works is the current operator of this facility, which produces salt through a process 

of solar evaporation. The salt works consists of a series of diked ponds (Figure F-2) that are 

designed to facilitate the concentration and ultimate precipitation of salts from bay water. Once 

seawater is taken from the bay, it is moved between the ponds through pumping and gravity flow. 

Approximately 60,000 to 80,000 tons of common salt (sodium chloride) are produced each year at this 

facility. This salt is sold commercially and used for water softeners, nitrate removal, ion exchange, 

pickling, deicing, as a dying additive, brine for petroleum products, and in the tuna industry as a 

means of controlling brine temperatures. Another salt produced as a byproduct of solar salt 

production is magnesium chloride, which is purchased by several industrial users in the area. 

The evaporation ponds that form this solar salt operation can be divided into four categories based 

on specific gravity, which is defined as the ratio of the mass of a sample of seawater to the mass of 

an equal volume of pure water (Stadtlander and Konecny 1994). The four categories of ponds 

include the primary system, secondary system, crystallizer system, and the heavy brine or bittern 

ponds (refer to Figure F-2). Throughout the solar salt production industry, salinities in salt ponds 

are measured using a hydrometer scale, which describes salinity in degrees Baume (°Be) rather 

than specific gravity. A more common way of describing salinity would be in terms of total 

dissolved solids or parts per thousand (ppt). The conversion from °Be to total dissolved solids 

(TDS) or ppt is: TDS = (13 x °Be) – 21 (Siegel and Bachand 2002). In terms of TDS, the average 

salinity value for seawater is 35 ppt (Siegel and Bachand 2002). In San Diego Bay, salinity levels 

can be quite variable, particularly at the south end of the bay. Mean salinity within the south bay 

between July 1994 and April 1999 ranged from 31.6 ppt in April 1998 to 38.6 ppt in October 1996 

(Allen 1999). 
Appendix F ──────────────────────────────────────────────

F-2 San Diego Bay National Wildlife Refuge ─────────────────────────────── 
Appendix F ──────────────────────────────────────────────

──────────── Final Comprehensive Conservation Plan/Environmental Impact Statement F-3
Appendix F ──────────────────────────────────────────────

F-4 San Diego Bay National Wildlife Refuge ─────────────────────────────── 

To produce salt within the salt pond system, bay water is introduced into the primary pond system, 

which includes Ponds 10A and 10 through 15, through a tide gate located between the Otay River 

and Pond 10. This gate is pressure-regulated opening and allowing intake of water when the tidal 

level in the river is higher than the pond level. As the tidal level in the river lowers, the water 

pressure on the pond side closes the gate. As the water moves through this primary system, it is 

transported from Pond 11 to Pond 12 via a 30-inch siphon pipe that extends under the Otay River. 

The water is moved through the primary pond system via gravity flow as the appropriate salinity 

levels are reached in each pond. By the time the incoming seawater has reached the end of the 

primary system, the salinity has increased from 3.5 °Be to between 7 and 10 °Be or 70 to 109 ppt 

(Western Salt Company 1997). Once in the system, the water in the ponds is often referred to as 

brine. The depth of the primary ponds varies due to topographic variation within each pond, as 

well as due to seasonal variations in volume of water present in each pond. Although the average 

depth in these ponds is approximately three feet, the water level in Pond 10A can be significantly 

lower and during some parts of the year, the bottom of the pond may be exposed. During the 

intake of bay water into the system, a variety of fish and crustacean species enter the primary 

system, where they are able to tolerate the slightly increased salinities of bay water within the 

initial ponds of the primary system. 

As needed, the brine is lifted by pump to the secondary system (Ponds 20 through 27), which 

consists of a series of smaller ponds. As the brine moves through the system, the salinities 

increase from 7 °Be to 19.5 °Be (70 to 232 ppt). Pond depths range from two to five feet at center. 

At about 12.9 °Be (147 ppt) gypsum, a crystal formed from the chemical precipitation of calcium 

and sulfate to form calcium sulfate, begins to precipitate from the water column forming a gypsum 

crust on the bottom of the ponds (Siegel and Bachand 2002). While attempting to survey the 

bottom elevations of these ponds, Ducks Unlimited engineers discovered that the gypsum crust in 

these ponds is highly irregular, with formations reminiscent of those gypsum formations found in 

Mono Lake. 

At the end of the secondary system are the pickling ponds (Ponds 28, 29 and 30), which have 

salinities that range from between 15 °Be and 25.5 °Be (174 to 310 ppt). These ponds are used to 

distribute the concentrated brine into the crystallizer ponds. It is also in this part of the system 

that most of the remaining gypsum precipitation occurs. At about 25.5 °Be (310 ppt) the brine is 

saturated with sodium chloride and bittern salts (more soluble salts and ions consisting primarily 

of chloride, magnesium, sulfate, potassium, and bromide) and is ready to be introduced to the 

crystallizer system. 

Precipitation of sodium chloride occurs within the crystallizer ponds (Ponds 40 through 48 and 50 

through 52), which have salinities ranging from 25.5 to just under 29 °Be (310 to 356 ppt). (It should 

be noted that although Ponds 40 and 50 through 54 are not located within the refuge boundary, 

these areas are currently leased by the salt works operator for use in the existing solar salt 

operation.) Once the salt has precipitated out, the pond is drained and the salt is removed from the 

crystallizer ponds with heavy equipment such as front-end loaders. 

Brine is eliminated from the crystallizer ponds before it reaches 29 °Be because brine of less than 

29 °Be and brine of 29 °Be or greater do not mix. This situation can result in uneven crystal 

development. The brine discharged from the crystallizer ponds is referred to as heavy brine or 

bittern, which has a salinity of 29 to 30 °Be (356 to 369 ppt). Bittern is comprised of sodium 

chloride, magnesium sulfate and magnesium chloride. Sodium chloride and magnesium sulfate 

continue to be precipitated out in this part of the system, leaving magnesium chloride in a liquid 

state that is sold to local industry. The salts that precipitate out during this process are harvested 
Appendix F ──────────────────────────────────────────────

──────────── Final Comprehensive Conservation Plan/Environmental Impact Statement F-5

and deposited into an unused production pond before being redistributed throughout the system 

(Western Salt Company 1997). 

Once the salt is removed from the crystallizer ponds, it is transported to the washer complex where 

it is washed and rinsed. It is then moved to a stockpile for drying and then processed for sale in 

bags or shipped in bulk as needed to commercial and industrial users.

References Cited

Allen, L.G. 1999. Fisheries Inventory and Utilization of San Diego Bay, San Diego California. 

(Final Report – Sampling Periods July 1994 – April 1999). 

Gustafson, Angie and Carrie Gregory. 2001. Historic Resource Evaluation Report for Western 

Salt Company Salt Works, San Diego County, Chula Vista, California. EDAW, San Diego, CA. 

Siegel, S.W. and P.A.M. Bachand. 2002. Feasibility Analysis of South Bay Salt Ponds Restoration, 

San Francisco Estuary, California. Wetland and Water Resources, San Rafael, California. 

Stadtlander, D. and J. Konecny. 1994. Avifauna of South San Diego Bay: The Western Salt Works 

1993-1994. U.S. Fish and Wildlife Service, Coastal Ecosystems Program, Carlsbad, CA. 

Western Salt Company. 1997. South Bay Salt Making, Chula Vista, CA. 
 

Appendix G 

Federal and State Ambient Air Quality 

Standards 
Concentration 3 Method 4 Primary 3,5 Secondary 3,6 Method 7

1 Hour 0.09 ppm (180 μg/m3

) 0.12 ppm (235 μg/m3

)

8

8 Hour — 0.08 ppm (157 μg/m3

)

8

24 Hour 50 μg/m3

150 μg/m3

Annual 

Arithmetic Mean 20 μg/m3

50 μg/m3

24 Hour 65 μg/m3

Annual 

Arithmetic Mean 12 μg/m3 Gravimetric or Beta Attenuation 15 μg/m3

8 Hour 9.0 ppm (10mg/m3

) 9 ppm (10 mg/m3)

1 Hour 20 ppm (23 mg/m3

) 35 ppm (40 mg/m3)

8 Hour 

(Lake Tahoe) 6 ppm (7 mg/m3

) — — —

Annual 

Arithmetic Mean — 0.053 ppm (100 μg/m3

)

1 Hour 0.25 ppm (470 μg/m3

) —

Annual 

Arithmetic Mean — 0.030 ppm (80 μg/m3

) —

24 Hour 0.04 ppm (105 μg/m3

) 0.14 ppm (365 μg/m3) —

3 Hour — — 0.5 ppm (1300 μg/m3

)

1 Hour 0.25 ppm (655 μg/m3

) — — —

30 Day Average 1.5 μg/m3 — — —

Calendar Quarter — 1.5 μg/m3 Same as 

Primary Standard

High Volume 

Sampler and Atomic 

Absorption

No 

Sulfates 24 Hour 25 μg/m3

Ion Chromatography

Federal

Hydrogen 

Sulfide 1 Hour 0.03 ppm (42 μg/m3

)

Ultraviolet 

Fluorescence Standards

Vinyl 

Chloride 9 24 Hour 0.01 ppm (26 μg/m3

)

Gas 

Chromatography

California Air Resources Board (7/9/03)

Inertial Separation 

and Gravimetric 

Analysis

Non-Dispersive 

Infrared Photometry 

(NDIR)

None

Non-Dispersive 

Infrared Photometry 

(NDIR)

Same as 

Primary Standard

Sulfur 

Dioxide 

(SO2)

Ultraviolet 

Fluorescence

Same as 

Primary Standard

No Separate State Standard

Same as 

Primary Standard

Carbon 

Monoxide 

(CO)

Fine 

Particulate 

Matter 

(PM2.5)

Gravimetric or 

Beta Attenuation

Extinction coefficient of 0.23 per kilometer — 

visibility of ten miles or more (0.07 — 30 

miles or more for Lake Tahoe) due to 

particles when relative humidity is less than 

70 percent. Method: Beta Attenuation and 

Transmittance through Filter Tape.

8 Hour 

Visibility 

Reducing 

Particles

See footnotes on next page ...

Atomic Absorption

Gas Phase 

Chemiluminescence

Nitrogen 

Dioxide 

(NO2)

Same as 

Primary Standard

Gas Phase 

Chemiluminescence

Lead9

Spectrophotometry 

(Pararosaniline 

Method)

Inertial Separation 

and Gravimetric 

Analysis

Ambient Air Quality Standards

Pollutant Averaging 

Time

Ozone (O3)

Ultraviolet 

Photometry

Ultraviolet 

Photometry

California Standards 1Federal Standards 2

Respirable 

Particulate 

Matter 

(PM10)
1. California standards for ozone, carbon monoxide (except Lake Tahoe), sulfur dioxide (1 and 24 hour),

nitrogen dioxide, suspended particulate matter—PM10, PM2.5, and visibility reducing particles, are 

values that are not to be exceeded. All others are not to be equaled or exceeded. California ambient air 

quality standards are listed in the Table of Standards in Section 70200 of Title 17 of the 

California Code of Regulations.

2. National standards (other than ozone, particulate matter, and those based on annual averages or 

annual arithmetic mean) are not to be exceeded more than once a year. The ozone standard is

attained when the fourth highest eight hour concentration in a year, averaged over three years, 

is equal to or less than the standard. For PM10, the 24 hour standard is attained when the expected 

number of days per calender year with a 24-hour average concentration above 150 μg/m3 is equal

to or less than one. For PM2.5, the 24 hour standard is attained when 98 percent of the daily

concentrations, averaged over three years, are equal to or less than the standard.

Contact U.S. EPA for further clarification and current federal policies.

3. Concentration expressed first in units in which it was promulgated. Equivalent units given in 

parentheses are based upon a reference temperature of 25°C and a reference pressure of 760 torr. 

Most measurements of air quality are to be corrected to a reference temperature of 25°C and a 

reference pressure of 760 torr; ppm in this table refers to ppm by volume, or micromoles of 

pollutant per mole of gas.

4. Any equivalent procedure which can be shown to the satisfaction of the ARB to give equivalent 

results at or near the level of the air quality standard may be used.

5. National Primary Standards: The levels of air quality necessary, with an adequate margin of safety to

protect the public health.

6. National Secondary Standards: The levels of air quality necessary to protect the public welfare 

from any known or anticipated adverse effects of a pollutant.

7. Reference method as described by the EPA. An “equivalent method” of measurement may be used 

but must have a “consistent relationship to the reference method” and must be approved by the EPA.

8. New federal 8-hour ozone and fine particulate matter standards were promulgated by U.S. EPA 

on July 18,1997. Contact U.S. EPA for further clarification and current federal policies.

9. The ARB has identified lead and vinyl chloride as 'toxic air contaminants' with no threshold level of 

exposure for adverse health effects determined. These actions allow for the implementation of 

control measures at levels below the ambient concentrations specified for these pollutants.

California Air Resources Board (7/9/03)
 

Appendix H 

 Air Quality Calculations
2600 V Street  Sacramento, CA 95818-1914  tel. 916 737.3000  fax 916 737.3030 

www.jonesandstokes.com

September 30, 2004 

Ms. Victoria Touchstone 

U.S. Fish and Wildlife Refuge Complex 

6010 Hidden Valley Road 

Carlsbad, CA 92009 

RE: Air Emission Estimates for the South Bay Salt Works (Requisition 1168040039) 

Dear Ms. Touchstone: 

As you requested, Jones & Stokes has generated emission estimates for two restoration 

alternatives (14 scenarios) described in the Sweetwater Marsh and South San Diego Bay Units of 

the San Diego Bay National Wildlife Refuge draft Comprehensive Conservation Plan and 

Environmental Impact Statement. 

The emission estimates were generated to determine whether either of the project’s alternatives 

would generate construction-related emissions that exceed the federal conformity thresholds for 

criteria pollutants, specifically reactive organic gases (ROG), carbon monoxide (CO), nitrogen 

oxides (NOx), or particulate matter less than 10 microns in diameter (PM10). At this time, a 

conformity analysis is not required for PM2.5. 

The emission estimates were based on information provided for each restoration alternative, 

which included project schedule, soil import/export estimates (cubic yards of material), 

estimated truck trips needed to haul material, and estimates of the type and numbers of 

construction equipment that would be used for individual project phases. This information was 

to generate estimates of exhaust emissions and fugitive dust (PM10) generation. Exhaust 

emissions included on-road vehicles; such as trucks used to haul material on- and off-site, vendor 

trips, and worker commute trips. Exhaust emissions also included off-road construction 

equipment emissions. 

The California Air Resources Board’s (ARB) EMFAC2002 model was used to generate 

estimates of on-road vehicle emissions. Off-road emissions were based on ARB’s off-road 

construction model. A modified version of the road construction emissions model was used to 

generate estimates of fugitive dust emissions and worker commute trips. 

The emission estimates generated for each scenario are summarized in the following table. They 

show that each of the alternatives would generate emissions substantially below the federal 
2600 V Street  Sacramento, CA 95818-1914  tel. 916 737.3000  fax 916 737.3030 

www.jonesandstokes.com

2 

conformity thresholds applicable within the San Diego Air Basin. Consequently, a conformity 

determination would not be required for this project. 

TONS PER YEAR 

Options ROG CO NOx PM10

Otay Option 1 only 1 9 11 4 

Otay Option 1 and Salt Works Option 1 3 23 27 10 

Otay Option 1 and Salt Works Option 2 3 25 28 8 

Otay Option 2 only 2 16 16 4 

Otay Option 2 and Salt Works Option 1 4 29 32 9 

Otay Option 2 and Salt Works Option 2 4 30 32 9 

Salt Works Option 1 only 2 14 15 5 

Salt Works Option 2 only 2 15 16 6 

Restored Salt Ponds 1 8 11 5 

Restored Salt Ponds + Otay Restoration Option 1 3 18 22 10 

Restored Salt Ponds + Otay Restoration Option 2 3 24 27 9 

Restored Salt Ponds (Breach) 2 11 13 5 

Restored Salt Ponds (Breach) + Otay Restoration Option 1 3 21 25 10 

Restored Salt Ponds (Breach) + Otay Restoration Option 2 4 27 30 9 

Conformity Threshold (tons/year) 100 100 100 100 

Please let me know if you have any questions or concerns regarding these emission estimates. 

Sincerely, 

Tim Rimpo 

Air Quality Project Director 
 

Appendix I 

Hydrodynamic Modeling Analysis
Lower Otay River Salt Marsh 

and Wetland Restoration:

Hydrodynamic Modeling Analysis 

Prepared for 

The United States Fish and Wildlife Service

and

Ducks Unlimited, Inc.

Prepared by

Philip Williams & Associates, Ltd.

October 1, 2003

PWA Ref. 1594
Services provided pursuant to this Agreement are intended solely for the 

use and benefit of The United States Fish and Wildlife Service and Ducks 

Unlimited.

No other person or entity shall be entitled to rely on the services, 

opinions, recommendations, plans or specifications provided pursuant to 

this agreement without the express written consent of The United States 

Fish and Wildlife Service and Ducks Unlimited in coordination with 

Philip Williams & Associates, Ltd., 720 California Street, 6th Floor, San 

Francisco, CA 94108.
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TABLE OF CONTENTS

Page No.

1. INTRODUCTION 1

2. LOWER OTAY RIVER PROJECT SETTING 2

2.1 Hydrologic and Geomorphic Setting 2

2.2 Project Site Characteristics 3

2.3 Restoration Objectives, Site Opportunities and Constraints 4

3. HYDRODYNAMIC MODELING DEVELOPMENT 6

3.1 Modeling Approach 6

3.2 Data Sources 6

3.2.1 Topography 6

3.2.2 Hydrology 7

3.2.2.1 Tidal Hydrology for Hydraulic Modeling 7

3.2.2.2 Surface Runoff Hydrology 8

3.3 Using Data Sources to Develop Input Model Parameters 9

3.4 Existing Conditions Model 10

3.4.1 100-Year Flood Results 10

3.4.2 Typical Diurnal Tide Cycle Results 11

3.4.3 Consideration of Geomorphology & Habitat 12

4. ALTERNATIVES ANALYSIS 13

4.1 Developing Alternatives 13

4.2 Alternative C (Option 1) 14

4.2.1 Configuration 14

4.2.2 Results 15

4.3 Alternative C (Option 2) 17

4.3.1 Configuration 17

4.3.2 Results 17

4.4 Alternative 3 (Hydraulic Improvements to Existing Otay Channel) 17

4.4.1 Configuration 17

4.4.2 Results 18

4.5 Alternative 5 (Pond 20A: Levee Removal and Grading) 19

4.5.1 Configuration 19

4.5.2 Results 19

4.6 Sediment Entraiment and Potential Scour Evaluation 19

4.7 Tidal Considerations for Alternatives 21

4.7.1 Tidal Hydrodynamics Under Restored Conditions 21

4.7.2 Geomorphic Adjustments to Lower Otay River 21

5. SUMMARY AND RECOMENDATIONS 23

6. LIST OF PREPARERS 24
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7. REFERENCES 25

8. FIGURES 26

LIST OF TABLES

Table 3-1. Published Tidal Datums for NOAA Tide Gage No. 9410170 in San Diego Bay 7

Table 3-2. Summary of FEMA Published Peak Discharges for the Otay River 9

Table 3-3. Manning’s Roughness Coefficients (n) 9

Table 3-4. Volumetric Overflow of Planning Unit A During 100-Year Flood Existing Conditions 11

Table 4-1. Changes in Wetland Area Associated with each Alternative 15

Table 4-2. Comparison of Peak Water Surface Elevations Under 100-Year Flow Conditions 16

Table 4-3. Excavation and Disposal Volumes Required for Wetland Restoration 16

Table 4-4. Alternative C: Comparison of Water Surface Elevations with/without Channel 

Improvements of Alternative 3 18

Table 4-5. Comparison of Velocity Conditions at RR Bridge (100-yr flood conditions) 20

Table 4-6. Comparison of Potential Scour at RR Bridge (100-yr flood conditions) 21

Table 4-7. Tidal Prism and Channel Depth Based on Hydraulic Geometry 22

LIST OF FIGURES

Figure 2-1. General Vicinity and Otay River Watershed Map

Figure 2-2. Historic Site Conditions

Figure 2-3. Planning Unit A Restoration Site Map

Figure 2-4. Topographic Map of Project Site

Figure 2-5. FEMA FIS Flood Map

Figure 2-6. Planning Unit A Site Characteristics

Figure 2-7. Planning Unit A Site Characteristics - RR Bridge

Figure 3-1. Synthesized Diurnal Tide Cycle for San Diego Bay

Figure 3-2. Representative Spring-Neap Tide Cycle for San Diego Bay

Figure 3-3. Existing Conditions Model Schematic

Figure 3-4. Graphical Representation of the 100-Year Flooding Sequence on Planning Unit A

Figure 3-5. Flooding Sequence for Table 3-4 (Existing Conditions)

Figure 3-6. Water Level Upstream of RR Bridge (Existing Conditions)

Figure 4-1. Alternative C (Option 1) Model Configuration

Figure 4-2. Water Surface Profiles of Lower Otay River for Existing Conditions and 

Alternatives

Figure 4-3. Water Surface Profiles of Nester Creek for Existing Conditions and Alternatives

Figure 4-4. Reference Locations for Tables 4-3 and 4-4 Comparing 100-yr Water Surface 

Elevations

Figure 4-5. Alternative C (Option 2) Model Configuration
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Figure 4-6. Alternative 3 (Hydraulic Improvements to Existing Otay Channel) Model 

Configuration

Figure 4-7. Alternative 5 (Pond 20: Levee Removal and Grading)

Figure 4-8. Simulated Water Levels Upstream of RR Bridge

Figure 4-9. Simulated Water Levels at Nester/Otay Confluence

Figure 4-10. Hydraulic Geometry for California Salt Marshes - Depth and Tidal Prism

Figure 4-11. Hydraulic Geometry for California Salt Marshes - Area and Tidal Prism
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1. INTRODUCTION

The U.S. Fish and Wildlife Service (FWS) and Ducks Unlimited (DU) contracted Philip Williams & 

Associates (PWA) to conduct a hydraulic analysis of the Lower Otay River, within Planning Unit A of 

the South San Diego Bay Unit of the San Diego National Wildlife Refuge. More specifically, PWA 

evaluated potential changes in flooding conditions associated with wetland restoration alternatives. FWS 

and DU staff had developed general alternative concepts for Planning Unit A to enhance and restore tidal 

and freshwater wetland habitats. PWA translated these general restoration concepts into representative 

surface and channel models of the site for use in the hydraulic analysis. PWA developed a onedimensional hydrodynamic model to simulate surface water elevations for existing conditions and project 

alternatives. 

Section 2 of this report describes the project site’s physical setting and introduces restoration

opportunities at regional and site-specific scales. Section 3 describes the hydraulic analysis including a 

discussion of the modeling approach, data sources, and modeling results for the existing baseline

condition. In Section 4, restoration alternatives developed by the DU/FWS team are presented and

compared to the baseline condition in terms of water surface elevations, changes in wetland area,

excavation volume required, and potential scour conditions near the railroad bridge. In Section 5, this 

report concludes with a discussion of next steps to continue the restoration effort of the Lower Otay River 

site.
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2. LOWER OTAY RIVER PROJECT SETTING

2.1 HYDROLOGIC AND GEOMORPHIC SETTING

The Otay River watershed is located in southwestern San Diego County encompassing approximately 143 

square miles (Figure 2-1). From its mouth at the southern end of San Diego Bay, the elongated pearshaped basin extends 25 miles east into the Cleveland National Forest. The maximum watershed

elevation is 3,300 ft at White Mountain. The Otay basin is bordered by the Telegraph and Sweetwater 

basins to the north and the Tijuana watershed to the south. The Otay watershed includes two water 

supply reservoirs (Upper and Lower Otay Reservoirs), which influence downstream hydrologic

conditions. The upper watershed (upstream of the reservoirs) is comprised of steep mountainous slopes 

with mostly igneous and metamorphic substrate. The steep tributary channels of the upper watershed 

have slopes averaging from 3 to 6%. Downstream of Savage Dam (Lower Otay Reservoir) tributary 

channels are generally less steep with average slopes between 2 to 3%. The western lower portion of the 

watershed is generally underlain by marine sediments that have been uplifted to create the characteristic 

mesa landscape. In the vicinity of the Highway 5 bridge crossing (towards the project site), the Otay 

River has a channel slope of less than 1% and is generally a sand and cobble bed stream. Towards the 

project site, bed materials tend towards finer sands, silts, and ultimately muds upon reaching the estuarine 

zone. The majority of the upper Otay watershed is unincorporated, but the lower watershed includes 

portions of the cities of Chula Vista, Imperial Beach, Coronado, National City, and San Diego. 

The lower Otay River project site (between the Highway 5 crossing and San Diego Bay) represents a 

transitional hydrologic zone between a fluvial dominated riverine system upstream and a tidally

dominated estuarine system downstream. As such, the project site involves a complex mixing of

freshwater, brackish, and tidal flows and hosts a mosaic of habitat types. An early map of San Diego Bay 

from 1859 (Figure 2-2) provides an excellent reference to understand how the system functioned

historically prior to subsequent impacts. As seen in the map of Figure 2-2, in 1859 the Otay river mouth 

was a deltaic feature that sloped northwesterly towards San Diego Bay. Three to four principal drainage 

channels crossed the deltaic plain, with the central bolder channel most likely being the direct conduit to 

the Otay River upstream. Depending upon the frequency and magnitude of episodic flood events, these 

principal channels would have shifted across the deltaic marsh plain. The hachuring, in Figure 2-2, 

between the principal channels indicates a tidal marsh environment that was regularly inundated. 

Towards the bay-ward fringe of the salt marsh, smaller tidal-slough type channels are seen that would 

have conveyed ebb and flood tides to and from the outer marsh plain. 

Since the 1859 mapping, several significant impacts to the lower Otay River project area impaired its 

hydrologic, geomorphic, and ecologic functioning as a river-mouth/delta/marsh plain complex. The more 

significant of these impacts include: (1) constructing several dikes and levees to support salt ponds north 

of the project site; (2) relocating and reshaping of Otay and Nestor creeks through the project area; (3) 
Lower Otay River Salt Marsh and Wetland Restoration PWA - 3

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construction and operation of railroad dyke and bridges through the project area; (4) placing up to several 

feet of fill in a variety of places within the project site, to support agricultural practices; and (5) 

developing and operating a sanitation treatment plant in the 1950s and 1960s which was later reduced and 

transformed into a pumping station and pipeline. 

2.2 PROJECT SITE CHARACTERISTICS

The Planning Unit A site is bordered by levees and ponds of The Western Salt Works Company to the 

west, northwest, and north; and Interstate-5 to the east. The southern project boundary bisects the Pond 

20A site, Nestor Creek, and joins Interstate-5 near the southern most of the two Otay River bridge 

crossings (Figure 2-3). The Planning Unit A site is approximately 140 acres. The Pond 20A site is 

approximately 110 acres; 68 acres of which are administered under the authority of the Port of San Diego 

and 32 acres administered by the FWS. While Pond 20A is not formally a piece of the National Wildlife 

Refuge, for future planning and restoration purposes it is useful to consider Pond 20A in coordination 

with Planning Unit A. Topographically, the project site is generally flat, with a gradual slope from the 

southeast to the northwest (Figure 2-4). Ground elevations range from roughly 18 ft (NAVD88) near the 

Interstate-5 crossing and along the tops of the surrounding levees (Pond 20A and Western Salt Works 

levees) to approximately 6 ft (NAVD88) within Pond 20A. The channel profile of the Otay River ranges 

in elevation from about 8 ft (NAVD88) near Interstate 5 to –2 ft (NAVD88) at the San Diego Bay 

confluence.

The project site contains two river channels: Otay River and Nestor Creek. The Otay River enters the site 

from the east (beneath Interstate 5) then flows to the northwest for approximately 2500 feet before turning 

sharply to the west, and then southwest (south of the levee-salt ponds system to the north). From this 

point downstream to San Diego Bay, the river is bound by the salt pond levees, which constrain the river 

to the north (and to the east and west further downstream towards the Bay). Previous modeling analyses, 

observed flood levels, and published FEMA Flood Insurance Studies all indicate that during extreme 

flood events, excess flows from the Otay River will overtop this levee system at several locations and 

flood the neighboring salt works. FEMA Flood Insurance Rate Maps (FIRM) for the project area are 

shown in Figure 2-5.

Nestor Creek, a comparatively small tributary to the Otay River, conveys local runoff from the

community of Nestor, northward under Palm Avenue and flows east of Pond 20A until it joins the Otay 

River. FEMA (FIRM maps 060732C2153F, 060732C2154F) indicate that the urban community near 

Nestor Cr. north of Palm Avenue (in the vicinity of Boundary Ave., Canal St., and Thermal Ave.) is 

mapped as being inundated by the 100-yr flood event (Zone AE: base flood elevations determined. 

Within the project area, the 100-yr event causes overbank flooding out from Nestor Cr. towards the east 

and towards Pond 20A to the west (Figure 2-5).

Downstream of the Otay River/Nestor Creek confluence, the Otay River channel is confined between the 

Pond 20A levee to the south and the salt works levees to the north, resulting in a hydraulic constriction 
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(Figure 2-6). At 1000 ft downstream of the Nestor Creek confluence, the Otay channel splits into two 

parallel reaches, separated by the abandoned San Diego & Eastern Railway line. This side-by-side 

channel configuration (as seen in Figure 2-4) that is split by the railway line continues for roughly 1500 

feet until the two parallel channels join and leave the Planning Unit A project site to the west. The 

railway line within this 1500 ft segment is supported by a dyke and two trestle bridges (Figures 2-7). The 

Otay River then continues to flow approximately one mile northwest and then north, discharging into 

South San Diego Bay.

Between Nestor Creek and the Otay River channel is a broad flat floodplain expanse (Figure 2-6). This 

floodplain, which historically formed a significant portion of the Otay River fresh and saltwater wetlands, 

was filled in the early 20th century to facilitate agricultural uses of the site. Today, this portion of the 

project site consists of very little vegetation, limited habitat and no fresh or saltwater wetlands. 

Tidal flows influence the Planning Unit A site, enter from San Diego Bay and extend up the Otay River to 

approximately 1500 feet upstream beyond the Nestor Creek confluence. This inland tidal extent was field 

verified by the appearance of tidal mud flats, which typically indicate the presence of daily inundation. 

The wildlife refuge also experiences seasonal or intermittent flows from Otay River and Nestor Creek. 

These flows may come in the form of extreme flood events with discharges exceeding 25,000 cfs. Such 

stormflows have the potential to modify the site through channel scour, levee overtopping and/or

breaching, and sediment deposition. Tidal and fluvial characteristics related to the modeling analysis are 

described in greater detail below in Section 3.

2.3 RESTORATION OBJECTIVES, SITE OPPORTUNITIES AND CONSTRAINTS

Developing an appropriate restoration concept for the lower Otay River project area requires an

understanding of the complex hydrologic processes occurring at the site. Additionally, the restoration 

concept should incorporate an appreciation of how historic processes and features governed the site over 

the longer term and consider how recent impacts have altered the physical system, reduced habitat areas, 

and impaired ecologic functioning. The principal objectives for a restoration project at the lower Otay 

River site include:

• Restoration of functioning wetland habitat (tidal, freshwater, brackish) in areas that have become 

drier uplands

• Enhancement of existing wetland areas to increase circulation and improve habitat conditions

• Develop a sustainable, relatively self-maintaining wetland design

• Maintain or decrease current flood elevations to avoid exacerbating predicted flood conditions in 

the vicinity of the project

• Minimize environmental impacts and excavation and earth work costs associated with restoration

• Develop a restoration plan that is flexible enough to integrate other regional restoration efforts 

including the restoration of the south San Diego Bay salt ponds.
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Current conditions at the lower Otay River (Planning Unit A) site provide both positive opportunities for 

restoration, as well as, limitations (or constraints) to reaching a successful restoration. Many of the site’s 

primary physical, natural resource, and planning opportunities and constraints were described in the 

MKEG Wetland Enhancement Plan (Michael Brandman Associates, 1989). The key physical

opportunities and constraints based upon Lower Otay River Wetland Enhancement Plan report include: 

Opportunities

• Expanded tidal circulation is feasible

• Seasonal freshwater flows from Otay River and Nestor Creek can potentially support in-channel 

habitat

• Groundwater is available to support riparian vegetation

• Flood hazard reduction is also achievable through ecologic/habitat restoration

• Increased tidal prism on site will help reduce on-site sedimentation and channel in-filling

• Soils underlying fill historically supported salt marsh vegetation and could likely do so again 

successfully after restoration 

• Site topography can be modified (with fill removed or relocated) to restore appropriate wetland 

elevations

Constraints

• Freshwater flows delivered by Otay River and Nestor Creek are episodic and infrequent

• Groundwater is slightly brackish potentially limiting vegetation to species with salt tolerance

• Extreme flood events may deliver large amounts of sediment to the project site (as observed in 

1916) 

• High groundwater levels might require special grading and excavating techniques

• Existing site elevations are high enough that a comprehensive wetland restoration effort would 

require extensive grading and earth moving

• Much of site is designated as a FEMA Floodway, potentially limiting the scope of work done on 

the site
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3. HYDRODYNAMIC MODELING DEVELOPMENT

3.1 MODELING APPROACH

PWA used the hydrodynamic module of MIKE 11 to evaluate the hydraulic conditions of the Lower Otay 

River, Nestor Creek and South San Diego Bay. MIKE 11 is a one-dimensional hydrodynamic model, 

developed by the Danish Hydraulics Institute (DHI), which solves the vertically integrated conservation 

of mass and momentum equations (Saint-Venant equations). For the Otay setting, the model expands 

upon basic channel hydraulics by more realistically portraying interactions between river and creek

channels, salt ponds, overbank floodplains, and the dynamic tidal and hydrologic boundary conditions. 

This added complexity allows the model to more accurately represent current site conditions and evaluate 

site conditions under different alternative configurations. However, it is important to remember that the 

hydraulic model developed for this study is at best an analytical tool used to simulate flow conditions and 

does not depict actual events.

3.2 DATA SOURCES

A number of existing information sources were collected and reviewed to provide input to the present 

hydrodynamic analysis. Project data were compiled into a spatial database (GIS) by thematic type 

(coverages) using ArcGIS software. This included site topography for existing and proposed alternative 

conditions and both tidal and surface runoff hydrology. The following sections describe these different 

input data sets.

3.2.1 Topography

The baseline topographic data used for this analysis was collected using differential GPS equipment and 

compiled into an AutoCAD contour map (1-foot resolution) by Ducks Unlimited Inc. This information 

was collected in 1999 and 2000 as part of a broader survey of the entire wildlife refuge area, salt works,

and surrounding areas. Certain additional data were collected in June 2002 (as requested by PWA) 

including supplemental ground topography along the project boundary, additional channel cross-sections 

and invert measurements, and a more detailed survey of bridge crossings. All topographic data were 

collected in the State Plane (California Zone VI - feet) horizontal datum and North American Vertical 

Datum 1988 (NAVD88 - feet) vertical datum.

The GPS field survey data were integrated with the baseline contour maps to develop an ArcGIS

Triangular Irregular Network (TIN). This TIN was used to generate a surface model which became the 

topographic foundation for the existing conditions model (Section 3.4). All MIKE 11 cross-sectional 

information for the existing conditions model was extracted from this surface model. For the alternatives 

analysis, the baseline surface model was modified according to the restoration concepts. Planform

channel alignments and grading adjustments were made in accordance with the restoration concepts 
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provided by FWS and DU (Appendix A). Similar to the digital terrain model developed for existing 

conditions topography, an ArcGIS TIN surface was developed for each alternative.

 

3.2.2 Hydrology

As a transitional estuary setting, the lower Otay River and wildlife refuge site are subject to tidal and river 

flows. These flows form the boundary conditions for the hydrodynamic model. These boundaries were 

limited to tides in San Diego Bay and river discharge from the Otay River and Nestor Creek. Other 

localized runoff sources were not considered significant relative to the volume and discharge of tides and 

river flows and were not included in the present analysis. The following sections present the tidal and 

surface runoff hydrology conditions adopted for the current modeling analysis and any limitations

associated with their use.

3.2.2.1 Tidal Hydrology for Hydraulic Modeling

The tidal flows in San Diego Bay can be characterized by diurnal (daily) and spring-neap (monthly) 

variations, which inundate the bottom portion of the Otay River and Nestor Creek channels twice daily. 

Considered independently, these tidal flows do not increase water level on the project site enough to flood 

overbank areas that were historically salt marsh and fluvial wetlands. 

Tidal hydrology reference levels refer to statistical stillwater tidal conditions in San Diego Bay and forms 

the downstream water level boundary condition for the hydrodynamic model. The National

Oceanographic and Atmospheric Administration (NOAA) operates and maintains a long-term primary 

tide gage (9410170) located at Navy Pier near downtown San Diego. This gage, which has been in 

operation since 1900, is approximately 9 miles north of the project site. Tidal measurements collected 

over a previous tidal epoch (19-year period from 1960 – 1978) have been statistically reduced to obtain 

long-term average values of Mean Lower Low Water (MLLW), Mean Lower Water (MLW), Mean Tidal 

Level (MTL), Mean Higher Water (MHW), and Mean Higher High Water (MHHW). Table 3-1 presents 

the two published tidal datums for San Diego Bay.

Table 3-1. Published Tidal Datums for NOAA Tide Gage No. 9410170 in San Diego Bay

Mean Tidal Tidal Statistics for San Diego Bay (Feet)

Datum Local MLLW Datum NAVD88 Datum

MHHW 5.73 5.08

MHW 4.98 4.33

MTL 2.96 2.31

MLW 0.94 0.29

MLLW 0.00 -0.65

Tidal datums presented in Table 3-1 were converted into a representative tide cycle for San Diego Bay. 

This was accomplished by applying a cosine interpolation to each neighboring published tidal datum from 

Table 3-1 at a 5-min time interval. The result of this analysis is presented in Figure 3-1 which represents 
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a typical diurnal tide cycle for San Diego Bay. A monthly tide cycle (Figure 3-2) exhibiting spring-neap 

variations was also developed using Tides & Currents Software (1993) and the published NOAA datum 

conversion from MLLW to NAVD88 or -0.65 feet.

According to the FEMA Flood Insurance Study (FIS) for San Diego County, California (Unincorporated 

Areas, January 2001), the 100-year water surface elevation for San Diego Bay at Chula Vista is 7.08 feet 

(NAVD88). Due to various coastal flooding mechanisms (e.g. river runoff, wind, storm surge), this 

published flood elevation is 2 feet higher than the representative MHHW datum used to form the tidal 

boundary condition for the present river flooding analysis. While acknowledging this difference, the 

MHHW datum was adopted as the high water tidal boundary condition to maintain consistency between 

the modeling analysis and upstream riverine flood insurance studies which use the 5.08 ft datum. For 

example, the current Otay River FEMA analysis uses the 5.08 ft MHHW datum as a downstream

boundary condition. The current PWA analysis is consistent with Otay River FEMA study.

3.2.2.2 Surface Runoff Hydrology

In contrast to the tides which inundate the lower Otay River daily, watershed derived runoff to the Otay 

River and Nestor Creek is relatively sparse throughout the year. However, during extreme rainfall events, 

the runoff typically exceeds channel capacity and flooding occurs throughout the project site. Following 

a thorough review by PWA of available hydrologic data sources, it was determined that no compatible 

stream gage data was available within the Otay River watershed, nor had a comprehensive hydrologic 

analysis been previously completed. This was supported by a phone conversation with Joe Evelyn (Chief 

of Hydrology and Hydraulics Division, Army Corps of Engineers, Los Angeles District) who was 

reasonably certain that no such hydrologic analysis has ever been performed. Furthermore, several

requests to FEMA to obtain the hydrology associated with the surrounding flood insurance studies

provided no additional information as of the completion of this report. 

In place of a comprehensive watershed derived hydrologic analysis or a complete statistical analysis of 

stream gage measurements, a simple equilateral triangular hydrograph (SCS method) was adopted. With 

the triangular hydrograph, storm duration was 24 hours, base flow was 10 cfs, and the peak discharge 

corresponded to the published FEMA 100-year stream flow. FEMA peak discharges were referenced 

from the most recent FEMA Flood Insurance Study1 (FIS) for the reach of the lower Otay River through 

Planning Unit A (Table 3-2). A second triangular hydrograph was similarly developed for Nestor Creek. 

Nestor Creek and Otay River peak flows were modeled to occur simultaneously to simulate maximum 

flooding conditions on the site. The lower flow regime for the lower Otay River is significantly impacted 

by the upstream reservoir, which stores much of the low flows with no release. It does not impact the 

predicted major floods, as the available storage is small in comparison to the predicted flood volumes.

 

1

 FEMA Flood Insurance Study, January 19, 2001, San Diego County, Unincorporated Areas
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Table 3-2. Summary of FEMA Published Peak Discharges for the Otay River

Published FEMA Peak Discharge (cfs)

Return Period

Otay River Nestor Creek

10 1200 730

50 12000 990

100 22000 1135

500 50000 3630

3.3 USING DATA SOURCES TO DEVELOP INPUT MODEL PARAMETERS

Using the data sources described above, a model drainage network schematic was developed for the 

project site (Figure 3-3). The schematic included a delineation of the likely flow paths (channels, 

overbanks, ponds, levee overflows, etc.) and their flow relationship (inter-connection) to one another. In 

addition, the location of each cross-section was assigned to the network. This cross-sectional information 

was extracted and compiled into the MIKE-11 cross-section database, using the appropriate topographic 

surface as discussed in Section 3.2.1.

Following the development of a representative model schematic, channel roughness characteristics were 

assigned. Estimates of Manning’s roughness coefficients (n) for the open channel portions were assigned 

based on field evaluations. Manning’s n values for roughness varied according to in-channel or overbank 

positions and varied spatially across the project site according to existing or anticipated (for the

alternatives) roughness conditions. Roughness designations for specific types of conditions (i.e.

immediate overbank levee area, or channel bottom in mud) were held consistent for the alternatives. 

Roughness values for the mature marsh condition were used in modeling Alternatives C1 and C2. 

Manning’s roughness values used in the numerical model are presented in Table 3-3. Modeled roughness 

values were consistent with the roughness coefficients applied in the FIS1.

Table 3-3. Manning’s Roughness Coefficients (n)

San Diego Bay 0.02

Otay Bridge 0.07

Otay Channel Bypass 0.06

Nestor Creek 0.06

Floodplain Areas 0.04

Boundary conditions were prescribed at three locations within the model drainage network representing 

tidal conditions in San Diego Bay (Section 3.2.2.1) and river discharges from Otay River and Nestor 

Creek (Section 3.2.2.2). As noted earlier, all other localized runoff was considered non-significant 

compared to the combined volume and discharge of water from the tides and river flows.
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3.4 EXISTING CONDITIONS MODEL

An existing conditions model was developed for Planning Unit A of the lower Otay River project area 

between Palm Avenue to the south, Interstate 5 to the east, and the Western Salt Company salt pond 

levees and San Diego Bay to the north and west. The model includes 12 channels interconnected by 50 

linking channels and 110 cross-sections. Figure 3-3 shows the location and extent of the channel network 

and cross-sections superimposed on a recent aerial photo. Two calculations were made using the existing 

conditions model: (1) an extreme flood event caused by 100-year river flows in Nestor Creek and the 

Otay River; and (2) a typical daily tidal cycle with no river discharge. The following two sections (3.4.1 

and 3.4.2) describe the results of these analyses.

3.4.1 100-Year Flood Results

The extreme flood event simulation consists of 100-year flows occurring simultaneously for the Otay 

River and Nestor Creek with a typical daily tide cycle as a downstream boundary condition. The model 

was run for four days. Days 1 and 2 provided a spin-up time to achieve equilibrium tidal conditions 

throughout the model. The flood hydrographs were introduced on the third day, with the final day 

remaining to allow for complete draining of the system. Peak flows from Otay River and Nestor Creek 

were modeled to occur simultaneously with MHHW as shown in Figure 3-4.

Localized overbank flooding begins almost immediately with the onset of the flood event. As water 

levels continue to rise in the project site, flooding is further aggravated by the hydraulic constriction

between the Pond 20A levee to the south and the salt works levees to the north. Relative to the hydraulic 

constriction caused by the Pond 20A levee (south) and the salt works levees (north), the railroad features 

(dyke and bridges) are not as significant as these other levees under the 100-yr flood condition for the 

existing topographic condition. 

As shown in Figure 3-4, water levels continue to rise upstream of the constriction until overflow into the 

neighboring salt ponds begins. At flows of about 8000 CFS (approximately 25-year event) the salt works 

levees begin overtopping 4 to 5 hours after the initiation of the flood event (depending on the location and 

height of the levees). After about 10 hours into the flood event, the Pond 20A levees to the south are also 

overtopped. The maximum flood crest elevation (17.9 ft, NAVD88) at the confluence of Nestor Creek 

and the Otay River occurred roughly midway through the flood event at a time of 12 hours. From this 

point, water levels began to recede slowly draining the project site. Approximately 27 hours after the 

flooding began, and 3 hours after the river returned to baseflow conditions, the project site was 

completely drained and the diurnal tide cycle, which was the downstream boundary condition,

predominated. Figure 3-4 provides a graphical representation of the flooding sequence. Modeling results 

indicate that Pond 20A is flooded mainly from Nestor Creek overflow. In Section 4 below, results for the 

alternatives are presented whereby Pond 20A is not flooded for alternatives C1, C2, Alt 3 and Alt 5. 

Potential flooding is also reduced along the Otay River (Figures 4-2 and 4-3).

 
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Much of the 100-year flow volume for Otay River and Nestor Creek (combined) is not contained within 

the project site during a 100-year event. As flood levels overtop the neighboring salt works levees, over 

60% of the event’s flow volume is lost to the north. Table 3-4 and Figure 3-5 indicate volumetric losses 

and the locational sequence of overflowing based on the existing conditions model.

Table 3-4. Volumetric Overflow of Planning Unit A During 100-Year Flood Existing

Conditions

Overflow Location Volume (ac-ft) Flooding Order

A 1321.0 1

rst

B 0.0 no overtop

C 6188.3 4

th

D 4563.9 2

nd

E 302.3 5

th

F 1504.9 3

rd

Total Overflow 13880

Total Model Inflow 23413

% of Total Inflow Lost to 

Neighboring Salt Works

59.3

PWA sought to verify existing conditions modeling results by comparing water surface elevations with 

published findings in the FEMA FIS. However, since the FEMA model was based upon a different 

modeling approach than the current PWA study (steady-state versus dynamic) and used different 

downstream boundary conditions, comparing results from the two studies is not considered meaningful. 

Section 4 below includes a discussion of potential scour conditions at the railroad bridge under existing 

and alternative conditions.

3.4.2 TypicalDiurnalTide Cycle Results

Results from the typical tidal analysis indicate that without modifications to the existing topography, the 

diurnal tide cycle will not exceed bankfull conditions. Furthermore, the maximum inland extent of the 

tides was predicted to be roughly 11,500 feet from the river mouth or approximately 1,500 feet upstream 

from the confluence of the Otay River and Nestor Creek. No direct verification was preformed for this 

calculation, although field observations and surveyed mud-line information (correlating to the MHW to 

MHHW range) supported modeling estimates. Figure 3-6 provides a graph of existing tidal water levels 

on the Otay River (just upstream of the railroad bridge) compared to downstream tides in San Diego Bay. 

This graph indicates some degree of tidal muting on the ebb tide. The role of tidal muting and its 

potential influence on the alternatives is discussed below in Section 4.7. 
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3.4.3 Consideration of Geomorphology & Habitat

It is useful to consider the existing conditions model in terms of geomorphology and habitat since this 

model provides the comparative basis for the alternatives analysis. Since both fluvial and tidal processes 

shape the existing Otay River channel, a long-term equilibrium channel geometry should exist whereby 

inputs/outputs of water and sediment are relatively balanced for fluvial and tidal sources. This geometry 

is best represented by historic conditions, when anthropogenic features did not strongly impact channel 

conditions. Such conditions, as illustrated in the 1859 map of Figure 2-1, indicate that a long-term 

geomorphically stable system would include a large deltaic marsh plain originating from the river source 

upstream. This marsh plain would include both freshwater and tidal wetlands, with the predominance of 

salt marsh increasing towards the Bay fringe. 

Watershed alterations during the past century have significantly altered the hydrologic regime of the 

lower Otay River. The reservoir captures upstream sediment and reduces freshwater flows to the 

downstream channel reaches and the Bay. Concurrently, urbanization and other land use changes have 

affected the hydrology, sediment and water quality regime in the lower river. Urbanization around the 

project site perimeter is located in the floodplain, and is subject to damage during the design (100-year) 

storm.

The current lower Otay River configuration represents a significantly altered condition from the longterm geomorphic model. This is very evident in considering that areas inundated by tides under current 

conditions represent less than 1% of the historically inundated regions in the project area. Such

reductions in tidal areas directly equate to reductions in habitat area and quality. Improving hydrologic 

and ecologic conditions at the existing Planning Unit A site is the goal of the subsequent alternatives 

analysis.
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4. ALTERNATIVES ANALYSIS

4.1 DEVELOPING ALTERNATIVES

Four conceptual design alternatives for the lower Otay River project area were analyzed and compared to 

the baseline conditions model. The initial planning and development of the alternatives was conducted by 

FWS with review and suggestions provided by DU and PWA. FWS and DU provided PWA with general 

descriptions of the alternatives with conceptual site maps that included the principal restoration elements. 

These maps are shown in Appendix A. In general, the alternatives differ in: (1) the relative allocation of 

restored tidal or freshwater wetland habitats; (2) the alignment of channels; (3) the degree of earth moving 

and levee modification; and (4) project costs. 

Based on the concepts shown in the alternative maps of Appendix A, PWA developed new surface 

topography (ArcGIS TIN) and representative channel cross sections to apply in the hydraulic modeling 

process. PWA also added a number of refinements in translating the alternative concepts shown in the 

Appendix A maps into more developed depictions of future site conditions. This process included

refining channel geometry conditions and defining tidal slough channels and other wetland topographic 

elements. In refining these alternatives, PWA maintained consistency with the overall restoration goals of 

the project (Section 2.3). These are reiterated as follows:

• Restoration of functioning wetland habitat (tidal, freshwater, brackish) in areas that have become 

drier uplands

• Enhancement of existing wetland areas to increase circulation, improve habitat conditions

• Develop a sustainable, relatively self-maintaining wetland design

• Maintain or decrease current flood elevations to avoid exacerbating predicted flood conditions in 

the vicinity of the project

• Minimize environmental impacts and excavation and earth work costs associated with restoration

• Develop a restoration plan that is flexible enough to integrate other regional restoration efforts 

including the restoration of south San Diego Bay salt ponds.

The alternative concepts provided to PWA characterize the project site into three habitat regions: salt 

marsh, freshwater wetland, and restored uplands. These generic habitat types represent fundamentally 

different topographic, hydrologic, geomorphic, and ecologic conditions. 

A restored salt marsh encompasses the full range of intertidal marsh habitats between mean lower low 

water (MLLW) and mean higher high water (MHHW). These include the low marsh region (dominated 

by intertidal mudflats (+3.5 ft MLLW and below) and cordgrass (Spartina foliosa) (generally +3.5 to +4.5 

ft MLLW)); the middle and high marsh (dominated by perennial pickleweed (Salicornia virginica) above 

+4.5 ft MLLW); and a high marsh/fluvial transition zone including a diverse assemblage of other salt 
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marsh plants. Most likely, channel geometry in this transitional zone is governed by tidal processes 

below MHHW and fluvial processes above (Mead et. al, 2000). In addition to the main Otay River and 

Nestor Creek channels, smaller tidal slough channels would be excavated throughout the proposed salt 

marsh plain area below the MLW level. The number and dimensions of these slough channels would be 

based on the sustainable area of tidal mud flats within the project site.

Freshwater wetland habitats also have a range of forms including: in-channel freshwater marshes; riparian 

woodland in the immediate channel bank and overbank floodplain zone; riparian scrub on the higher 

floodplain elevations; and a transitional zone to upland (non wetland) vegetation at higher elevations. 

Restored upland areas provide important buffering, foraging, and refuge functions to the neighboring 

wetland areas and also provide a useful depositional area for removed fill from potential site excavation. 

Four alternatives are presented below. The first two involve different habitat configurations across the 

Planning Unit A site, while the third one focuses solely on channel improvements to the lower Otay 

River. The fourth presented alternative considers removal of a portion of the Pond 20A levee. The 

naming of these alternatives is adopted from FWS designations. Since there was originally a pool of 

several more alternatives, the alternatives that were selected for the modeling study have their original 

names below and do not follow an intuitive or sequential (A, B, C or 1, 2, 3) naming order.

4.2 ALTERNATIVE C (OPTION 1)

4.2.1 Configuration

Alternative C (Option 1) comprises widening the existing Otay River channel and significantly expanding 

both tidal and freshwater wetlands (Appendix A, Figure 4-1). To compensate for the excavation required 

to re-establish these wetlands, areas of restored upland are included to balance on-site cut and fill 

volumes. Thus, the design configuration of this alternative will minimize off-site earth disposal and its 

associated costs.

For Alternative C (Option 1), the basic alignment of the Otay River would remain unchanged, flowing 

generally northwestward to the edge of the existing salt works levee, then southwest, parallel to the levee, 

to the western edge of Pond 20A (Figure 4-1). The cross-sectional shape of the channel, however, would 

be significantly altered. The existing bankfull channel would be widened to approximately four times its 

current width. In the upper sections of the channel, fresh water wetlands would be re-established. A lowflow channel would be developed in this reach, with a meandering planform, that would slowly transition 

from fresh water wetland to salt water marsh and inter tidal mud flats. This re-established salt marsh area 

would be constructed with a similar widened channel configuration to the north along the salt works 

levee. The northern portion of the existing Pond 20A levee would also be removed and setback along the 

property line, thus creating additional tidal wetlands at the confluence of Nestor Creek. Soils excavated 

from the wetland areas of the site would be used to raise portions of the site previously identified as 

restored uplands. The volume of excavated soil in excess of that which can be accommodated on-site 

would be removed from the site, however for this alternative, off-site removal has been minimized.
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4.2.2 Results

The total area of re-established tidal and freshwater wetlands associated with Alternative C (Option 1) is 

78 acres, 61 of which would be salt marsh and 17 of which would be fresh water wetland. Under existing 

conditions, the only areas of sustained wetlands are within the channels themselves, amounting to less 

than 10 acres. Thus, Option 1 provides nearly a 1000% increase in wetland habitat area for Planning Unit 

A (Table 4-1). 

Table 4-1. Changes in Wetland Area Associated with each Alternative

Existing 

Conditions

Alternative C

(Option 1)

Alternative C

(Option 2)

Alternative 3 Alternative 5

Wetland 

Habitat

Area (acres) Area 

(acres)

% 

Increase

Area 

(acres)

% 

Increase

Area 

(acres)

% 

Increase

Area

(acres)

% 

Increase

Fresh 

Water

5 17 340 17 340 5 0 N/A N/A

Salt Marsh 3 61 2030 88 2930 3 0 N/A N/A

Total 8 78 975 105 1310 8 0 N/A N/A

 

Hydraulic results for Option 1 show that setting back the Pond 20A levee significantly increases

conveyance capacity of the Otay River, reduces backwater effects extending upstream, and ultimately 

lowers the 100-year flood elevations by more than one foot. Figure 4-2 shows this reduction in upstream 

flood levels along the Otay River channel. Additionally, Figure 4-2 demonstrates the change in water 

surface slope, from relatively steep through the Pond 20A constriction under existing conditions, to

generally flatter gradients when the Pond 20A levee is set back as part of the wetland restoration. 

Furthermore, because of this water level reduction, the upper portions of Pond 20A (south of the realigned 

levee) would not receive spill over from the Otay River under the modeled 100-year conditions. 

Significant overtopping of the salt works levees would still occur, however for a shorter period of time. 

Figure 4-3 shows water surface profiles for existing and alternative conditions along Nestor Creek, with 

lower water elevations under alternative scenarios. All of the alternatives show a reduced water level in 

Nestor Creek. The most significant decrease is shown with alternative C1 and results from removal of the 

levee along Pond 20. Water surface elevations for baseline and alternative conditions are compared for 

several locations below in Table 4-2. Comparison locations are referenced in Figure 4-4.
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Table 4-2. Comparison of Peak Water Surface Elevations Under 100-Year Flow Conditions

Existing 

Conditions

Alternative 

C

(Option 1)

Alternative 

C

(Option 2)

Alternative 3 Alternative 5

Location1

Peak Water Surface Elevation (ft – NAVD88)

A. Approximately 1000 feet 

downstream from the I-5 Bridge

18.8 18.0 18.1 18.7 18.0

B. Where the Otay River meets 

salt works levee system

18.2 16.8 16.7 18.1 16.6

C. Confluence of Otay River 

and Nestor Creek

Otay River

17.9 15.9 15.8 17.8 15.2

D. Northwestern edge of Pond 

20A

13.0 14.0 14.0 12.5 15.0

Nestor Creek

E. 2000 ft upstream of 

confluence with Otay River

18.2 16.9 17.8 18.1 17.5

1. See Figure 4-4 for comparison locations 

Alternative C (Option 1) requires approximately 645,000 cu yd of soil materials to be excavated and 

disposed from the project site. All of the excavated soil can be accommodated on site into 60 acres of 

restored upland areas. Table 4-3 summarizes the excavation and disposal conditions for 3 of the 4 

alternatives considered. Excavation volumes for Alternative 5 were not evaluated because a surface 

elevation model was unavailable (personal communication with Steve Carroll at DU).

Table 4-3. Excavation and Disposal Volumes Required for Wetland Restoration

Alternative C

(Option 1)

Alternative C

(Option 2)

Alternative 3 Wetland Creation1

Volume (cu-yd) Volume (cu-yd) Volume (cu-yd)

Total Excavation 726,000 968,000 32,266

Total On-site Disposal2726,000 322,666 0

Off-site Disposal 0 645,333 32,266

notes:

1. Excavation volumes calculated from GIS/CAD surface models discussed in Section 3.2.1.

2. On-site disposal will occur in areas designated as restored uplands.

3. Data for Alternative 5 are not available.
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4.3 ALTERNATIVE C (OPTION 2)

4.3.1 Configuration

Alternative C (Option 2) is generally similar to Option 1 involving an expansion of tidal wetlands and 

setting back the Pond 20A levee (Appendix A, Figure 4-5). However, Option 2 does not include 

widening the upper portion of the Otay River channel. Instead, a freshwater wetland will be developed 

east of the northern extension of Saturn Drive (and pipeline easement). To the west of the Saturn Drive 

extension, complete re-establishment of tidal marsh is envisioned. This expanded tidal wetland zone 

replaces the restored uplands from Option 1. As a whole, the Option 2 design configuration restores more 

tidal salt marsh than Option 1, however costs would be significantly greater due to increased off-site soil 

disposal requirements.

4.3.2 Results

Restored tidal and freshwater wetland areas for Alternative C (Option 2) are presented above in Table 4-

1. Option 2 (105 acres) provides 25% more restored habitat than Option 1 (78 acres). Whereas Option 1 

provided a balance between required excavation and on-site disposal, the additional 27 acres of new 

marsh for Option 2 results in about 645,333 cu-yd of off-site disposal (Table 4-3). In terms of the 

hydraulic impacts, water level conditions for Option 2 are very similar to Option 1 (Table 4-2). Option 

2’s modified planform and expanded tidal wetland does not significantly alter estimated flood stages from 

Option 1 results because water levels upstream of Pond 20A are again governed by the backwater effects 

from the hydraulic constriction. For example, where the Otay River meets the salt works levee system, 

predicted water levels for Options 1 and 2 differ by less than two inches.

4.4 ALTERNATIVE 3 (HYDRAULIC IMPROVEMENTS TO EXISTING OTAY CHANNEL)

4.4.1 Configuration

Alternative 3 is qualitatively different from the previous two alternatives. Rather than focusing on habitat 

and wetlands restoration, this alternative reduces downstream channel constrictions along the Otay River 

by widening the channel at a location that is geomorphically suitable and where land is available for 

excavation. Thus, the focus of this alternative is solely flood reduction. Figure 4-6 illustrates the location 

where channel widening was simulated for the modeling analysis. PWA chose this location during a site 

visit due its channel/overbank form. A benched terrace exists along this reach, which could be modified 

to accommodate a wider channel. Because flood reduction was the sole focus of Alternative 3, many of 

the restoration goals outlined previously were not addressed. However this analysis does provide insight 

into the effect downstream channel capacity has on upstream flooding. 
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4.4.2 Results

The overall results for Alternative 3 indicate that channel improvements alone do not significantly reduce 

flood levels throughout the project site. Because the Pond 20A levees were not set back as in the previous 

alternatives, the hydraulic constriction remained and upstream flood levels were only somewhat reduced 

through widening the channel further downstream. More substantial improvements would be needed 

along the entire length of the Lower Otay River channel, especially adjacent to Pond 20A, to provide a 

more substantial reduction in upstream flooding. A study completed by Rick Engineering (1987) looked 

at substantially modifying and improving the flood capacity of the lower Otay River channel. The Rick 

Engineering report suggested lowering and hardening a large portion of the salt works levee system to 

allow controlled overflow into the salt ponds. Although Alternative 3 and the alternative developed by 

Rick Engineering address flood reduction, they do not provide the appreciable habitat benefits of the 

Alternative C options. Tables 4-1, 4-2, and 4-3 also include results for Alternative 3.

The hydraulic improvements of Alternative 3 were combined with the expanded wetland configurations 

of Alternative C (Options 1 and 2) to evaluate the combined effect of enlarging the downstream channel 

and expanding the upstream wetland configuration. Results from this analysis indicate that upstream 

flooding would not be significantly affected, however downstream of Pond 20A, peak flood levels would 

decrease by roughly 1-foot (Table 4-4, locations referenced in Figure 4-4).

Table 4-4. Alternative C: Comparison of Water Surface Elevations with/without Channel 

Improvements of Alternative 3

Alternative C (Option 1) Alternative C (Option 2)

Location w/out Alt 3 with Alt 3 w/out Alt 3 with Alt 3

Peak Water Surface Elevation (ft – NAVD88)

A. Approximately 1000 feet 

downstream from the Interstate-5 

Bridge

18.0 18.0 18.1 18.1

B. Location where the Otay River 

meets the salt works levee system

16.8 16.7 16.7 16.7

C. Confluence of Otay River and 

Nestor Creek

15.9 15.8 15.8 15.9

Otay River

D. Northwestern edge of Pond 20A 14.0 13.6 14.0 13.3

Nestor 

Creek

E. Approximately 2000 feet upstream 

from confluence with the Otay River

16.9 16.8 17.8 17.8
Lower Otay River Salt Marsh and Wetland Restoration PWA - 19

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4.5 ALTERNATIVE 5 (POND 20A: LEVEE REMOVAL AND GRADING)

4.5.1 Configuration

The configuration of Alternative 5, shown in Figure 4-7, was developed by FWS/DU and described to 

PWA as follows. The portion of the Pond 20A levee that is located within the FWS Refuge Boundary is 

removed. The refuge land portion of Pond 20A is graded to achieve elevations that support intertidal 

habitat. Grading occurs to provide a marsh plain slope of approximately 10:1. The envisioned marsh 

plain consists of about 50% intertidal mud flat and 50% salt marsh habitat. Moving southward along the 

Pond 20A parcel, at the location/elevation that achieves MHHW, the slope gradient is changed to 2:1 

towards the southern boundary of the Refuge parcel. Grading would daylight at the refuge boundary. 

Additionally, Alternative 5 includes a shallow pilot channel breach from Nestor Creek into Pond 20A. A 

surface model for this alternative was not available to PWA, all topographic changes and conditions 

associated with the alternative were modeled based upon received descriptions of the alternative. 

Representative cross sections, which portrayed the alternative concept, were developed and input to the 

model.

4.5.2 Results

Results for Alternative 5 indicate that levee removal and marsh plain grading in Pond 20A significantly 

increases flow capacity through Pond 20A and results in decreased upstream flooding. Maximum water 

levels decrease by: 0.8 ft near the I-5 Bridge; 2.7 ft at the Nestor Creek confluence; and 1.9 ft at the Otay 

River salt works levee. However, by removing the Pond 20A northern levee, the railroad bridge channel 

zone at the northwest corner of Pond 20A would now function as a natural constriction point for the 100-

yr discharge. This process results in an estimated increase of surface water elevation by 2.2 ft near the 

railroad bridge. In this scenario, the bridge is exposed to higher discharge, pressure, and scour conditions. 

Under Alternative 5, additional bridge and channel modifications are recommended to increase flow 

capacity and channel/bridge structural integrity under the 100-yr event. It should be noted that the 

bikeway would be under water during the design (100-year) flood for both existing conditions and the 

alternatives discussed in this section.

4.6 SEDIMENT ENTRAIMENT AND POTENTIAL SCOUR EVALUATION 

Hydraulic conditions and the potential for sediment entrainment and channel scour were evaluated at the 

railroad bridge location for existing and alternative scenarios. The following methods for computation of 

maximum potential local scour were used:

a) Laursen – (1960)

b) Laursen modified - (1960)

c) Liu - (1961)

d) Froehlich - (1987)
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These equations are empirical and derived mostly with laboratory data. It is generally understood that 

scour estimates calculated using these equations tend to be greater than the scour observed in field 

conditions. The actual scour is affected by many variables including the degree of consolidation in

channel bed sediments. Also, scour increases other channel hydraulic parameters such as cross sectional 

area, hydraulic radius, velocity and depth, creating a feedback which modifies flow parameters to reduce 

the scour potential.

Additionally, three structural factors were considered that could influence the local scour calculation at 

the railroad bridge.

1. The degree of channel contraction, measured by channel width and structural opening (width of 

the structure, abutments length or cross sectional area).

2. The degree of increase in flow resistance in the culvert/bridge crossing (obstructed area) relative 

the main channel. (Laursen 1960). In the case of higher resistance inside of the bridge, the 

potential scour can increase by 100% or more.

3. The ratio of obstructed flow area to adjacent channel area. (Froehlich). This method indicates the 

highest potential scour, given the significantly narrowed flow area at the railroad crossing. 

The results from the scour analysis for the 100-yr flood event are summarized in Tables 4-5 and 4-6. 

Potential scour conditions for baseline and alternative conditions are compared for the 4 computational 

methods used in the analysis. These results should be considered as a basis for relative comparison rather 

than an assessment of absolute change, owing to the assumptions stated above. That being said, the 

percent changes for some alternatives exceed 20% increases from existing conditions and this is

noteworthy. In the case of Alternative 5, increases in flow velocity, discharge and water level at the 

bridge crossing should be considered in any site restoration design or re-design of the existing trestle 

bridge.

Table 4-5. Comparison of Velocity Conditions at RR Bridge (100-yr flood conditions)

RR Bridge Velocity Evaluation (ft/s) Existing Alt C1 Alt C2 Alt 3 Alt 5

Velocity at RR Bridge 5.8 8.4 8.5 6.9 11.2

% change from existing conditions + 44.6% + 46.9% + 18.6% + 92.66%

Velocity upstream of RR Bridge 4.8 4.4 7.2 6.2 8.2

% change from existing conditions -6.9% + 51.7% + 31.0% + 72.41%
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Table 4-6. Comparison of Potential Scour at RR Bridge (100-yr flood conditions)

RR Bridge Scour Evaluation (ft) Existing Alt C1 Alt C2 Alt 3 Alt 5

Larsen 1960 5.1 7.3 5.2 4.9 5.1

Larsen 1960 (modified) 3.0 4.8 3.0 2.8 2.7

Liu 1961 10.0 11.9 11.6 10.7 12.8

Froehlich 1987 20.8 23.4 23.2 21.7 25.9

average 9.7 11.8 10.8 10.1 11.6

% change from existing conditions - + 21.67% + 10.65% + 3.48% + 19.73%

4.7 TIDAL CONSIDERATIONS FOR ALTERNATIVES

The expected tidal functions of the four alternatives were compared to existing conditions in order to 

assess the feasibility of the proposed tidal restoration concepts. This initial assessment used the numerical 

model to simulate tidal hydrodynamics under restored conditions, as well as application of hydraulic 

geometry relations to predict the geomorphic response of lower Otay River. 

4.7.1 TidalHydrodynamics Under Restored Conditions 

Unlike the high-magnitude flood flows, the water level elevation of tidal inundation is not significantly 

affected by the hydraulic restrictions of the Otay River RR Bridge or its narrow channel between the salt 

works and Pond 20A levees. This is illustrated in Figure 4-8 which plots water surface elevations (just 

upstream of the RR bridge) under existing conditions and for each of the restoration alternatives. Figure 

4-9 plots water surface elevations at the Nester Creek/Otay River confluence and shows a similar pattern 

for high water inundation reaching the project area. 

These results show no significant muting for the flood tide water condition. However, low water drainage 

elevations are affected by the restoration alternatives during the ebb tide. This is presumably due to 

friction losses within the channels that are strongest during ebb flow when water depths decrease. 

Reduced low water drainage would not have a major effect on wetland establishment, and will improve as 

tidal scour deepens the main tidal channels (see discussion below). Alternatively, “starter channels” or 

other features could be included in the restoration design to accelerate development of an equilibrium 

main channel. 

4.7.2 Geomorphic Adjustments to Lower Otay River 

The morphology of the lower Otay River system will evolve after restoration due to an increase in tidal 

current velocities. Based on other restoration experience, we anticipate that increased tidal velocities will 

result in channel deepening (preferentially along the channel thalweg) until a new channel geometry

occurs which is in equilibrium with the systems tidal prism. Numerical simulation of erosion and
Lower Otay River Salt Marsh and Wetland Restoration PWA - 22

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sediment transport is difficult due to the variability of soil properties and the complexity of the physical 

processes. Therefore, PWA applied hydraulic geometry relations to estimate an anticipated amount of 

channel down-cutting along the main channel following tidal restoration.

Empirical relationships between tidal prism and channel geometry have been developed for coastal salt 

marshes based on survey data collected in San Diego Bay and San Francisco Bay (PWA, 1995). Given 

the existing morphology of the lower Otay River, a modest amount of down-cutting is expected along the 

thalweg after tidal restoration. Based on hydraulic geometry relationships (see Figure 4-10), we estimate 

that the channel bed will eventually deepen about 3 ft after tidal restoration, depending on which

restoration alternative is constructed (see Table 4-7). Estimates of the potential tidal prism were based on 

the footprint of the restored marsh area, and varied between 50 and 65 ac-ft for Alternatives C1 and C2 

(see Figure 4-11).

Cross sectional area of Otay River downstream of the restored marsh area is expected to increase by a 

factor of 3 to 4. The channel will initially deepen in the short-term in response to the additional tidal 

prism, with channel widening continuing at a slower rate. 

Table 4-7. Tidal Prism and Channel Depth Based on Hydraulic Geometry

Alternative Tidal Prism 

(ac-ft)

Channel Depth 

(ft below MHHW)

 Existing Conditions 6 5

 Alternative C1 50*

7.5

 Alternative C2 65*

8

* approximate potential tidal prism based on hydraulic geometry
Lower Otay River Salt Marsh and Wetland Restoration PWA - 23

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5. SUMMARY AND RECOMENDATIONS

The primary objective of this hydraulic analysis was to evaluate how potential restoration concepts for the 

lower Otay River area (Planning Unit A) might impact flooding conditions on site and in surrounding 

areas to the project site. Results from the hydraulic modeling suggest that the considered restoration 

alternatives would not negatively impact flooding conditions, but would most likely reduce potential

flooding hazards by reducing surface water elevations and durations (as indicated by the 100-yr design 

storm event). Modeling results indicated that increased channel capacity, either through levee setback or 

removal could provide moderate to significant additional benefits in flood reduction. As shown by

alternatives C and 5, the set back or removal of the Pond 20A levee significantly reduced upstream flood 

levels. Analysis indicated that each of the alternatives increase flow velocities, water elevations, and 

scour potential at the railroad bridge crossing. Additional engineering studies and potential refinement of 

the railroad bridge channel/bridge crossing design is recommended as part of the on-going planning and 

restoration process. In addition to these primary conclusions, PWA refined project alternatives to

maximize restored habitat areas while minimizing earth-moving costs.

While not modeled as part of this report, modifying or removing the Western Salt works levee system 

between the project site and the Bay is likely to significantly reduce the predicted flood levels at the 

project site and in upstream off-site areas. Additionally, eventually reconnecting the Planning Unit A and 

Western Salt Works areas would represent substantial progress towards restoring the historic geomorphic 

form and function of the lower Otay River floodplain and saltmarsh system, in which the channel mouth 

and adjacent wetlands function as a less constrained morphologic unit.

Building on the current study, PWA recommends moving into a more thorough restoration pre-design 

phase that will result in a well-defined project designed to preliminary standards that can be efficiently 

implemented. Although it is likely that additional environmental and technical aspects for a restoration 

program will need to be considered, in terms of hydrology/hydraulics, the following three issues are most 

compelling to support the restoration effort.

• Geomorphic analysis to develop a suitable channel size and network configuration. 

Channel density, depth, width, and sinuosity should be examined in terms of the expected 

long-term configuration. Additionally, this geomorphic analysis should be integrated into 

the design process in order to reduce the amount of earthwork required for restoration.

• Evaluation/refinement of bridge/channel crossing design based on hydraulic conditions of 

the alternatives.

• Integration of the current modeling analysis into the feasibility analysis of restoring the 

Salt Works areas north of Planning Unit A. Any hydrologic analysis of the potential salt 

pond restoration options should include the baseline modeling conditions developed for 

the current lower Otay River area.
Lower Otay River Salt Marsh and Wetland Restoration PWA - 24

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6. LIST OF PREPARERS

This report was prepared by the following PWA staff:

Jeffrey Blank, M.S. Hydraulic Modeling

Bo Juza, Ph.D. Hydraulic Modeling

Don Danmeier, Ph.D. Hydraulic Modeling

Kenneth Schwarz, Ph.D. Project Manager 

Jeffrey Haltiner, Ph.D., P.E. Project Director
Lower Otay River Salt Marsh and Wetland Restoration PWA - 25

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7. REFERENCES

Federal Emergency Management Agency (FEMA), 2001. Flood Insurance Study, San Diego County, 

Unincorporated Areas. January 19, 2001.

Mead et. al, 2000. Equilibrium Channel Geometry in a Tidally Influenced River Reach. Proceedings 

from the International Conference on Riparian Ecology and Management in Multi-Land Use 

Watersheds, American Water Resources Association, August, 2000.

Michael Brandman Associates and Philip Williams and Associates, Ltd., 1989. MKEG Wetlands 

Enhancement Plan. Prepared for the Southwest Wetlands Interpretive Association and the California 

State Coastal Conservancy. August 1989.

Nautical Software Inc., 1993. Tides & Currents Pro (Version 2.5l), Beaverton, Oregon, 1993.

Philip Williams and Associates, Ltd. (PWA), 1995. Design Guidelines for Tidal Channels in Coastal 

Wetlands. Prepared for the U.S. Army Corps of Engineers, Waterways Experiment Station. January 

1995.

Rick Engineering, 1987. Hydraulic Report for the Otay River Between Interstate 5 and the San Diego 

Bay. Prepared for MKEG. September 2, 1987.
Lower Otay River Salt Marsh and Wetland Restoration PWA - 26

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8. FIGURES
Appendix A

Planning Unit A: 

Conceptual Restoration Alternatives (FWS)
f i g u r e 2-1

General Vicinity and Otay River Watershed Map

Lower Otay River Salt Marsh and Wetland Restoration

Upper Otay 

Reservoir

Lower Otay 

Reservoir

Project Otay River

 Site

Pacific Ocean

San Diego

Bay
Historic Site Conditions

Lower Otay River Salt Marsh and Wetland Restoration

3.

f i g u r e 2-2

Source: Survey of the Coast of the United States, Coastal Survey Office, 1859.

±
UKL Daily Outflow (1973 – 1997)

USBR (Denver) Unimpaired Inflows - Gate Outlet 

Control

Planning Unit A Restoration Site Map

Lower Otay River Salt Marsh and Wetland Restoration

4.

f i g u r e 2-3

Pond 

20A

Otay 

River

Nestor 

Creek

South San 

Diego Bay

Western Salt Works 

Salt Ponds

Planning Unit A Refuge 

Management Boundary

Primary River Channels

Salt Works Levees

Pond 20 Levee

±

0 550 1,100 2,200 3,300 4,400

Feet
f i g u r e 2-5

FEMA FIS Flood Map

Lower Otay River Salt Marsh and Wetland Restoration
Topographic Map of Project Site

Lower Otay River Salt Marsh and Wetland Restoration

7.

f i g u r e 2-4

0 - -5

Elevation (feet)

30 - 25

25 - 20

20 - 15

15 - 10

10 - 5

5 - 0

-5 - -10

Note: All Elevations are in the NAVD 88 (feet) Vertical Datum

±

0 550 1,100 2,200 3,300 4,400

Feet
Planning Unit A Site Characteristics

Lower Otay River Salt Marsh and Wetland Restoration

8.

f i g u r e 2-6

Otay River – looking southwest between Pond 20 (near) and Salt Works Levee (far)

Otay River – looking southeast from Pond 20A (site of proposed marsh restoration)
Planning Unit A Site Characteristics – RR Bridge

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 2-7

Otay River RR Bridge downstream of Pond 20A
Synthesized Diurnal Tide Cycle for San Diego Bay

Lower Otay River Salt Marsh and Wetland Restoration

9.

f i g u r e 3-1

-1.00

0.00

1.00

2.00

3.00

4.00

5.00

6.00

Day 1 Day 2 Day 3 Day 4 Day 5

Time (days)

Water Level (feet) NAVD88
-2

-1

0

1

2

3

4

5

6

7

1 7 13 19 25 31

Time (days)

Water Level (feet) NAVD88

Representative Spring-Neap Tide Cycle for San Diego Bay

Lower Otay River Salt Marsh and Wetland Restoration

10.

f i g u r e 3-2
UKL Daily Outflow (1973 – 1997)

USBR (Denver) Unimpaired Inflows - Gate Outlet 

Control

Existing Conditions Model Schematic

Lower Otay River Salt Marsh and Wetland Restoration

11.

f i g u r e 3-3

0 - -5

Elevation (feet)

30 - 25

25 - 20

20 - 15

15 - 10

10 - 5

5 - 0

-5 - -10

Inter-connected “Link” Channels

Main River Channels

Cross-Section Locations

±

0 550 1,100 2,200 3,300 4,400

Feet
`

UKL Daily Outflow (1973 – 1997)

USBR (Denver) Unimpaired Inflows - Gate 

Outlet Control

f i g u r e 3-4

Graphical Representation of the 100-Year Flooding Sequence on Planning Unit A

Lower Otay River Salt Marsh and Wetland Restoration

0

5000

10000

15000

20000

25000

30000

35000

0.00 6.00 12.00 18.00 24.00 30.00 36.00

Time (hours)

Discharge (cfs)

Flood Crest (23135 cfs) 17.9' NAVD88

at the Confluence of Nestor Creek

and the Otay River (t = 12 hrs)

Pond 20 Begins to Flood

(t = 10 hrs)

Salt Works Levees Begin

to Overtop (t = 4 to 5 hrs)

Return to Baseflow

Conditions (t = 24 hrs)

Site Completely

Drained (t = 27 hrs)

Otay River 100-year

Discharge Hydrograph

Water Level

(feet) - NAVD88

6

-1

2.5

MHHW (5.08 ft)

MLLW (-0.65 ft)
South San 

Diego Bay

No 

overtop

1

rst

4th

5th

2nd

Flooding Sequence for Table 3-4 (Existing Conditions)

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 3-5

3rd

±

0 550 1,100 2,200 3,300 4,400

Feet
Water Level Upstream of RR Bridge (Existing Conditions)

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 3-6

-1.0

0.0

1.0

2.0

3.0

4.0

5.0

6.0

12:00 PM 6:00 PM 12:00 AM 6:00 AM 12:00 PM

Time

Elevation (ft - NAVD88)

Existing Conditions

Bay Tides
UKL Daily Outflow (1973 – 1997)

USBR (Denver) Unimpaired Inflows - Gate Outlet 

Control

Alternative C (Option 1) Model Configuration

Lower Otay River Salt Marsh and Wetland Restoration

12.

f i g u r e 4-1

0 - -5

Elevation (feet)

30 - 25

25 - 20

20 - 15

15 - 10

10 - 5

5 - 0

-5 - -10

Inter-connected “Link” Channels

Main River Channels

Cross-Section Locations

±

0 550 1,100 2,200 3,300 4,400

Feet
UKL Daily Outflow (1973 – 1997)

USBR (Denver) Unimpaired Inflows - Gate Outlet 

Control

Water Surface Profiles of Lower Otay River for Existing Conditions and Alternatives

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 4-2

0.0

5.0

10.0

15.0

20.0

25.0

0.0 2000.0 4000.0 6000.0 8000.0 10000.0 12000.0 14000.0

Distance (feet)

Elevation (feet - NAVD88)

Existing Conditions

Alt C1

Alt C2

Alt 3

Alt 5

Confluence with Nestor Creek

Downstream of Pond 20

Location where Otay River

Meets Salt Works Levees Interstate - 5

Bridge

Mouth of

Otay River
f i g u r e 4-3

Water Surface Profiles of Nestor Creek for Existing Conditions and Alternatives

Lower Otay River Salt Marsh and Wetland Restoration

15.0

15.5

16.0

16.5

17.0

17.5

18.0

18.5

19.0

0.0 2000.0 4000.0

Distance (feet)

Elevation (feet - NAVD88)

Existing Conditions

Alt C1

Alt C2

Alt 3

Alt 5

Confluence withOtay River
UKL Daily Outflow (1973 – 1997)

USBR (Denver) Unimpaired Inflows - Gate Outlet 

Control

Alternative C (Option 2) Model Configuration

Lower Otay River Salt Marsh and Wetland Restoration

15.

f i g u r e 4-5

0 - -5

Elevation (feet)

30 - 25

25 - 20

20 - 15

15 - 10

10 - 5

5 - 0

-5 - -10

Inter-connected “Link” Channels

Main River Channels

Cross-Section Locations

±

0 550 1,100 2,200 3,300 4,400

Feet
South San 

Diego Bay

Reference Locations for Tables 4-2 and 4-4 Comparing 100-yr Water Surface Elevations

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 4-4

A

B

C

D

E

±

0 550 1,100 2,200 3,300 4,400

Feet
Alternative 3 (Hydraulic Improvements to Existing Otay Channel) Model Configuration

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 4-6

Inter-connected “Link” Channels

Main River Channels

Cross-Section Locations

0 - -5

Elevation (fe et)

30 - 25

25 - 20

20 - 15

15 - 10

10 - 5

5 - 0

-5 - -10

±

0 550 1,100 2,200 3,300 4,400

Feet

Channel Widening Area
Alternative 5 (Pond 20: Levee Removal and Grading)

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 4-7

Inter-connected “Link” Channels

Main River Channels

Cross-Section Locations

±

0 550 1,100 2,200 3,300 4,400

Feet

Levee removal

Extend of marsh plain grading

Breach 
-1.0

0.0

1.0

2.0

3.0

4.0

5.0

6.0

12:00 PM 6:00 PM 12:00 AM 6:00 AM 12:00 PM

Time

Elevation (ft - NAVD88)

Existing Conditions

Alt C1

Alt C2

Alt 5

Bay Tides

f i g u r e 4-8

Simulated Water Levels Upstream of RR Bridge

Lower Otay River Salt Marsh and Wetland Restoration
0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

12:00 PM 6:00 PM 12:00 AM 6:00 AM 12:00 PM

Time

Elevation at Nester/Otay (ft - NAVD88)

-1.0

0.0

1.0

2.0

3.0

4.0

5.0

6.0

Elevation in Bay (ft - NAVD88)

Existing Conditions

Alt C1

Alt C2

Alt 5

Bay Tides

Note that different scales are used to plot the tides in South San Diego 

Bay and at the confluence of Otay and Nester Creeks.

f i g u r e 4-9

Simulated Water Levels at Nester/Otay Confluence

Lower Otay River Salt Marsh and Wetland Restoration
f i g u r e 4-10

Source: Philip Williams and Associates, Design Guidelines for Tidal Channels in 

Coastal Wetlands, Prepared for the U.S. Army Corps of Engineers, Waterways 

Experiment Station, January 1995.

Hydraulic Geometry for California Salt Marshes 

– Depth and Tidal Prism

Lower Otay River Salt Marsh and Wetland Restoration
Hydraulic Geometry for California Salt Marshes 

– Area and Tidal Prism

Lower Otay River Salt Marsh and Wetland Restoration

f i g u r e 4-11

Source: Philip Williams and Associates, Design Guidelines for Tidal Channels in 

Coastal Wetlands, Prepared for the U.S. Army Corps of Engineers, Waterways 

Experiment Station, January 1995.
 

Appendix J 

Desalinization and Brine Management 

Feasibility Assessment 
 Preliminary Feasibility Assessment 

of Desalinization and Brine Management 

for the South San Diego Bay Salt Ponds Restoration 

FINAL REPORT 

Prepared for 

Ducks Unlimited 

Prepared by 

Philip Williams & Associates, Ltd. 

with 

DHI Water & Environment 

May 9, 2003 

PWA REF. 1631 
Services provided pursuant to this Agreement are intended solely for the 

use and benefit of the Ducks Unlimited and the US Fish & Wildlife 

Service. 

No other person or entity shall be entitled to rely on the services, 

opinions, recommendations, plans or specifications provided pursuant to 

this agreement without the express written consent of Philip Williams & 

Associates, Ltd., 720 California Street, 6th Floor, San Francisco, CA 

94108.
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i 

TABLE OF CONTENTS 

Page No.

1. INTRODUCTION 1

2. KEY FINDINGS AND MANAGEMENT CONSIDERATIONS 2

2.1 Key Findings 2

2.2 Management Considerations 3

3. MODEL DEVELOPMENT AND CALIBRATION OF EXISTING CONDITIONS 5

3.1 Introduction and Modeling Objectives 5

3.2 Overview of the Numerical Models 5

3.3 Development of the Numerical Bay Model 6

3.3.1 Model Time Step, Extents and Grids 6

3.3.2 Hydrodynamics Model: Water Levels and Currents 7

3.3.3 Salinity Transport Modeling 8

3.4 Model Validation 9

3.4.1 Water Level Validation 9

3.4.2 Current Validation 10

4. SALINITY REDUCTION MODELING 12

4.1 Introduction 12

4.2 Alternatives Configuration 12

4.3 Results 14

4.3.1 Phase 2 14

4.3.2 Phase 3 15

4.4 Model Limitations and management considerations 16

5. BRINE FEASIBILITY 18

5.1 Configuration of the Brine Complex 18

5.2 The Box Model 19

5.3 Results 19

5.3.1 Brine Ponds 20

5.3.2 Mixing Basin 20

5.4 Model Limitations and Management Considerations 21

6. LIST OF PREPARERS 24

7. REFERENCES 25
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05/12/03

ii 

LIST OF TABLES 

Table 3-1. MIKE 21 Grid Specifications 7

Table 3-2. Depth Dependent Manning Numbers 7

Table 3-3. Comparison of Modeled Versus Measured Water Levels Tidal Constituents 11

Table 3-4. Comparison of Modeled Versus Measured Current Speed, for Tidal Constituent M2 11

Table 4-1. Initial Conditions: Pond Water Surface Elevations and Salinities Prior to Breaching 14

Table 5-1. Run Catalog for Box Model 23

LIST OF FIGURES 

Figure 1 Configuration of Restoration Alternative C Option 4 

Figure 2 Configuration of Restoration Alternative D 

Figure 3 Extents of MIKE 21 Nested Model Grids 

Figure 4 Location of MIKE 11 Otay River and Breach Weirs 

Figure 5 Bed Elevations for Salt Ponds 4 

Figure 6 Locations of NOAA Current Measurements During the 1983 Measurement Period 

Figure 7 Pond Salinity Time Series, Phase 2 

Figure 8 Salinity Distribution in the South Bay and Ponds, Phase 2, 1 day after breach 

Figure 9 Salinity Distribution in the South Bay and Ponds, Phase 2, 7 days after breach 

Figure 10 Salinity Distribution in the South Bay and Ponds, Phase 2, 28 days after breach 

Figure 11 San Diego Bay Salinity Point Locations 

Figure 12 San Diego Bay Salinity Time Series, Phase 2 

Figure 13 Salinity Distribution in the South Bay and Ponds, Phase 3, 1 day after breach 

Figure 14 Salinity Distribution in the South Bay and Ponds, Phase 3, 7 days after breach 

Figure 15 Salinity Distribution in the South Bay and Ponds, Phase 3, 28 days after breach 

Figure 16 San Diego Bay Salinity Time Series, Phase 3 

Figure 17 Configuration of Brine Complex 

Figure 18 Conceptual Layout of Box Model 

Figure 19 Monthly Mean Evaporation and Precipitation Rates for Chula Vista 

Figure 20 Time Series of Discharges and Salinity in Brine Ponds 

Figure 21 Time Series of Brine Pond Water Depths 

Figure 22 Time Series of Mixing Basin Discharges 

Figure 23 Flushing Time in Mixing Basin 
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1. INTRODUCTION 

The U.S. Fish and Wildlife Service (USFWS) is currently developing a Comprehensive Conservation 

Plan (CCP) and Environmental Impact Statement (EIS) for the South San Diego Bay Unit of the San 

Diego National Wildlife Refuge. This plan includes alternatives to restore and enhance habitat for aquatic 

and avian wildlife species within the 1,050-acre salt pond complex along South San Diego Bay. Ducks 

Unlimited (DU) is assisting the USFWS in the planning effort and contracted Philip Williams & 

Associates, Ltd. (PWA) to carry out a preliminary assessment of salinity reduction and feasibility of a 

managed brine complex. 

The restoration alternatives under development include various levels of tidal wetland restoration within 

the pond complex and reduction of acreages dedicated to commercial salt harvesting. USFWS and DU 

selected two specific alternatives for impact analysis that included restoration of many of the ponds 

fronting the bay to tidal inundation, and a reduced salt production operation (Alternative C Option 4, 

Figure 1) or complete elimination of salt production in favor of managed open-water and brine ponds 

(Alternative D, Figure 2). PWA conducted a preliminary technical assessment to answer the following 

key questions in support of the CCP and EIS process: 

• What are the short-term effects on salinity in San Diego Bay that would result from breaching 

salt pond levees for desalination, and how quickly can these ponds be flushed to ambient 

salinity levels? 

• Is the proposed brine operation feasible, given the flow rates required to maintain suitable 

habitat in the ponds and the necessary dilution of the hypersaline brine prior to discharge to 

the bay? 

PWA conducted hydrodynamic and salinity transport modeling of two salinity reduction scenarios and 

applied a simple box model of the brine operations to address the questions above. DHI Water and 

Environment (DHI) was sub-contracted to develop and apply the numerical hydrodynamic and salinity 

transport model in support of this analysis. 
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2. KEY FINDINGS AND MANAGEMENT CONSIDERATIONS 

2.1 KEY FINDINGS 

PWA conducted hydrodynamic and salinity transport modeling to assess changes in pond and Bay 

salinities that would result from breaching salt pond levees for salinity reduction. We modeled a phased 

salinity reduction approach for Alternatives C4 and D. Phase 1 consists of salinity reduction in Ponds 10, 

10A, and 11 (Figure 1). Phase 2 includes breaching of Ponds 12 – 15, assuming that the Phase 1 ponds are 

tidal and at ambient bay salinities (approximately 33 ppt). Alternative D (Figure 2) includes an additional 

third phase, in which Ponds 23-25 and 28-30 are breached once salinities in the Phase 2 ponds have 

reached ambient levels. Because of the limited number of model runs contracted for this study, we 

modeled salinity reduction for only Phases 2 and 3. Pond desalinization in Phase 1 is expected to occur 

more quickly and with fewer salinity effects to the Bay than in Phases 2 and 3 because of the smaller total 

mass of salt in the Phase 1 ponds. Key results from numerical modeling of the proposed salinity 

reduction alternatives include: 

• Salinities in the Phase 2 ponds can be reduced to 38 ppt (+5 ppt above ambient levels) within 

approximately one month. The rate of salinity reduction is initially rapid, then slows over time as 

the ponds equilibrate to the salinity of the bay. Once salinities decrease to 38 ppt, further salinity 

reduction is very gradual. Salinity reduction is slowest in Pond 13, the only pond that is not 

directly adjacent to the Bay. 

• The Phase 3 ponds drain almost completely on the first ebb tide and discharge into the Phase 2 

Ponds. From there, flushing from the Phase 2 ponds into the bay is similar to the flushing that 

occurs in Phase 2. Because the bottom elevations of the Phase 3 ponds are above high tide levels, 

the ponds are not re-flooded in subsequent tide cycles. Isolated “puddles” of high salinity water 

remain due to the micro-topography of the ponds. Some ditching or grading may be required to 

drain these puddles for desalinization. 

• Within San Diego Bay, salinity increases above 38 ppt (+5 ppt above ambient) are generally 

limited to areas south of the Chula Vista Nature Reserve and to the first week following 

breaching for both Phases 2 and 3. As expected, salinity effects are highest in the vicinity of the 

ponds and immediately after breaching. For Phase 2, salinities in the vicinity of the ponds peak at 

50 ppt during the first ebb tide, then decrease to approximately 40 ppt one day after breaching. 

For Phase 3, salinities in the vicinity of the ponds peak at 120 ppt during the first ebb tide, then 

decrease to approximately 60 ppt one day after breaching. As expected, salinity in the immediate 

vicinity of the ponds varies greatly over the tide cycle, with maximum effects observed during 

low tide, as hypersaline pond water is discharged into the bay. 

• Breach widths of approximately 5 meters appeared to provide a reasonable balance between 

rapidly reducing pond salinities and reducing initial salinity increases in the Bay. Mixing and 
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salinity reduction in Pond 13 during Phase 2 could be enhanced by adding additional breaches to 

Pond 14 or 15. The breach sizes were selected for the purposes of salinity reduction. Final breach 

sizes will be selected based on habitat considerations and may be refined in size and location 

from those used here. 

The preliminary feasibility assessment of the brine complex consisted of applying a box model to the 

proposed configuration of the brine ponds. The brine complex, located in the eastern part of the site, 

includes Ponds 42, 43, 45, 46, and 47 (Figure 2). We assumed that slightly hypersaline water (40 ppt) 

water from the managed ponds would serve as the source of inflow to the brine ponds and that the brine 

ponds would discharge to a mixing basin for dilution with Bay water to near ambient salinity levels (+ 5 

ppt) prior to discharge to the Bay. From this preliminary assessment, we conclude the following: 

• It appears feasible to manage the brine ponds to simultaneously meet the target salinities for 

habitat inside the ponds (80 – 120 ppt) and the target salinities for discharge to the Bay (discharge 

salinities below ambient + 5 ppt) using pumping. Required flow rates into the brine ponds and 

into the mixing basin for dilution are well within levels that can be accommodated by pumping. 

• Flow rates into the brine ponds vary seasonally from about 60 to 170 gpm over the course of a 

typical year, with the highest rates in the summer due to rapid evaporation. The flows must be 

managed seasonally to maintain the ponds within the target salinity range. Allowing the pond 

salinities to vary within the target range allows peak summer flow rates to be reduced below those 

that would otherwise be required to meet a constant pond salinity target. 

• Flow rates through the mixing basin (Pond 41) are much higher than those through the brine 

ponds, and vary between approximately 300 and 1300 gpm. These higher flow rates are needed 

to dilute the brine effluent to dischargeable levels and to offset the effects of evaporation in the 

mixing basin itself. Flushing times vary from 10 to 37 days. The peak flow rates could be 

reduced to about 830 gpm using flash mixing, in which brine outflow is rapidly diluted in a small 

basin or canal prior to discharge to the Bay. Flash mixing requires smaller flow rates since the 

effects of evaporation are negligible. However, dilution operations may need to be managed more 

closely in flash mixing since any variation in dilution rates would translate more quickly to 

salinity variations in waters released to the Bay. Despite the modest flow rates, operating costs 

may be large due to the continuous (or nearly continuous) pumping required. 

2.2 MANAGEMENT CONSIDERATIONS 

Application of the numerical model is useful for estimating pond desalinization times and characterizing 

the potential extent and magnitude of salinity effects in San Diego Bay. However, implementation of the 

salinity reduction program will also require adaptive management to respond to actual conditions during 

desalinization which may vary from predicted conditions for a variety of reasons. An adaptive 

management approach would include monitoring during desalinization and identification of adaptive 

actions, such as closing off the breaches, that could be applied if needed. It may also include staggering 
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the levee breaches so that tidal action is restored to the ponds one at a time. Model limitations and 

additional management considerations are discussed in Section 4.4. 

The brine management box model includes several simplifying assumptions for the purpose of 

preliminary feasibility assessment. If brine management is carried forward in project planning, these 

assumptions will need to be assessed in more detail later in the design process. Brine operations must be 

sufficiently flexible to prevent pond drying and levee overtopping for a range of climatological 

conditions, to maintain salinities within the target range for habitat, and to avoid hypersalinity and 

gypsum formation. Sufficient safeguards would be required to avoid high salinity discharges in the event 

of extreme wet and dry years, pump failure, or other atypical conditions. In addition, further analysis 

could be useful for identifying lower cost implementation approaches, particularly to reduce the cost of 

pumping. Model limitations and additional management considerations are discussed in Section 5.4. For 

the purposes of this study, we have assumed that inflow into the Brine complex is continuous. However, 

pumping rates that vary in a step-wise manner could be applied to the box model as well. 

This study addresses the spatial and temporal extent of salinity changes associated with desalinization and 

ongoing brine management. This information can be used to assess ecological or other potential impacts 

associated with the salinity changes. We understand that these issues will be addressed in subsequent 

environmental review and planning. The salinity reduction and brine management operations may be 

refined as needed once project impacts have been more clearly defined. 
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3. MODEL DEVELOPMENT AND CALIBRATION OF EXISTING CONDITIONS 

3.1 INTRODUCTION AND MODELING OBJECTIVES 

We applied numerical modeling to simulate salinity reduction associated with restoration of the South 

Bay Salt Ponds. The model is a combined one-dimensional/two-dimensional hydrodynamic and salinity 

transport model. We used the model to assess the time scales needed to lower salinity in the ponds and 

the effects on San Diego Bay salinities following the hypersaline discharges. 

We developed a Bay-wide numerical model that includes the entire San Diego Bay, the local offshore 

Pacific Ocean, the South Bay Salt Ponds and the tidal limits of the lower Otay River. The model is 

capable of predicting both the near-field (local) and far-field (regional) hydrodynamics and salinity 

impacts of high salinity discharges from breaching the salt ponds. 

Application of a depth-averaged 2D model over San Diego Bay and the ponds was assumed appropriate 

since the shallow water depths in the South Bay will lead to a fairly well-mixed water column. The 1D 

model was added to simulate the lower Otay River and pond breaches. 

3.2 OVERVIEW OF THE NUMERICAL MODELS 

The Bay-Wide numerical model uses a combination of DHI’s two-dimensional (MIKE 21) and onedimensional (MIKE 11) modules in order to simulate flows in San Diego Bay, the salt ponds, and the 

lower Otay River. The MIKE 21 and MIKE 11 components are dynamically coupled at boundary link 

locations through the MIKE Flood interface. PWA and DHI have successfully applied the MIKE Flood 

model for desalinization and restoration design modeling of the Napa River Salt Ponds in San Francisco 

Bay. The Napa River salt ponds are similar in configuration to the San Diego ponds and the model was 

used to answer similar types of salinity reduction questions. 

The numerical simulation of water levels and currents for the bay and ponds was carried out using MIKE 

21 NHD (Nested Hydrodynamic) modeling system. Salinity modeling was carried out using the MIKE 

21 NAD (Nested Advection-Dispersion) model. The NAD model runs dynamically coupled to the NHD 

model. The nested model includes the capability of allowing finer (smaller) local grids to be dynamically 

linked into coarser regional grids. 

 

The MIKE 11 model is used to model the tidal reach of the lower Otay River, and incorporates a river 

model previously developed by PWA for DU. Breaches are effectively earth weirs and are modeled using 

control structure weir components of MIKE 11. This allowed breach widths smaller than the grid 

resolution of the two-dimensional model. The MIKE 21 model is used to simulate the ponds and San 

Diego Bay. 
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The MIKE 21 and MIKE 11 models have been dynamically coupled in the Bay-Wide model using the 

MIKE Flood interface. At each computational time step, momentum and mass are transferred across link 

points that couple the two modules. For the present applications, link points were specified at each 

breach location and the at lower reach of the Otay River. 

3.3 DEVELOPMENT OF THE NUMERICAL BAY MODEL 

The model covers the entire San Diego Bay (Figure 3), and extends offshore from west of Point Loma to 

upstream of the tidal limit of Otay River. The modeling program consisted of the following steps: 

• model setup for existing conditions, 

• validation, and 

• scenario and production simulations. 

The model setup phase involves translating the physics into the mathematical schematization, based on 

measurements, observations and engineering judgment. Typically, calibration is then conducted to adjust 

model parameters so that the model prediction compares well with measured data. For this study, since 

the timeline was short and the San Diego Bay has been extensively modeled in the past, we used 

published data from existing calibrated models in the initial model setup and proceeded directly to the 

validation phase. Validation involves using the calibrated model setup for a new period of time on an 

independent dataset and checking that model predictions compare well to measurements. Model setup is 

described in this section; model validation is described in Section 3.4. 

We relied on calibration data available from Wang et al. (1998), who conducted an extensive 

hydrodynamic model calibration using measurements from NOAA from 1983. Other datasets were 

provided digitally from Dr. Ken Richter of Space and Naval Warfare Systems Command (SPAWAR), but 

time limitations on the project did not allow a treatment of these other sources. The current level of 

model calibration and validation is considered appropriate for this phase of project planning. See Section 

4.4 for a discussion of model limitations. 

3.3.1 Model Time Step, Extents and Grids

Model grids were developed from combined bathymetric and topographical databases available for the 

San Diego Bay area. Surveys by the US Navy on a 50-meter resolution were the main source of 

bathymetry data for the San Diego Bay. A more detailed description of the bathymetry and topography of 

the salt ponds complex was provided by DU in an AutoCAD DEM (Digital Elevation Model) (Figure 5). 

In order to increase the efficiency of the MIKE 21 model, a 25-meter grid of the Salt Ponds and southern 

reach of the bay was nested into a 75-meter grid that covered the entire Bay and nearshore zone (Figure 

3). Since lower Otay River and the pond breaches could not be resolved in the 25-meter grid, these 

elements were included in MIKE 11 and coupled to the larger MIKE 21 model using the MIKE Flood 

interface. Figure 4 shows the location of the MIKE 11 branch and link points as applied in the model. 
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The hydrodynamic model was setup to run with a time step of 5 seconds, a requirement for numerical 

stability in the AD (advection-dispersion) model. The exact dimensions and locations of the twodimensional model are listed in Table 3-1. 

Table 3-1. MIKE 21 Grid Specifications 

Grid 

Spacing 

Dimension 

X 

Dimension 

Y 

Origin 

Longitude 

Origin 

Latitude 

Orientation 

(m) (# points) (# points) (degree) (degree) (degree) 

75 281 231 -117.30364 32.58160 -0.163595 

25 181 193 -117.13425 32.58392 -0.073158 

3.3.2 Hydrodynamics Model: Water Levels and Currents

The main input parameters in the hydrodynamic model are: 

• Model geometry, bathymetry (discussed above) 

• Bed resistance (Manning’s number) 

• Eddy viscosity 

• Boundary conditions 

• Source/Sink input (i.e. power plant intake and discharge) 

3.3.2.1 Bed Resistance 

A depth dependent Manning n map was developed based on roughness values proposed by Wang et al. 

(1998) for San Diego Bay. Table 3-2 gives the depth relationship for the Manning’s number used in the 

model and taken from Wang 1998. 

Table 3-2. Depth Dependent Manning Numbers 

Water Depth 

(m, MSL) 

Manning’s n Values 

0.6 > depth 0.024 

2.0 > Depth > 0.6 0.022 

6.5 > Depth > 2.0 0.020 

12.5 > Depth > 6.5 0.018 

Depth > 12.5 0.015 

Source: Reprinted from Wang et al. 1998 
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3.3.2.2 Eddy Viscosity 

Experience with similar coastal systems suggests that the eddy viscosity values can be reasonably 

predicted by E ≅ K ∆x

2

/∆t, where E is eddy viscosity, K is an empirical constant that typically ranges 

between 0.01 and 0.06 (DHI, 2002), ∆x is grid spacing, and ∆t is the computational time setup. Although 

the model was not very sensitive to the eddy viscosity within these ranges of K, final calibrated values 

were selected to dampen unrealistic eddy patterns in the flow fields. The final values used a K of 0.02 

and give: 

 E = 22.5 m2

/s (75 meter grid) 

 E = 2.5 m2

/s (25 meter grid) 

3.3.2.3 Boundary Conditions 

As shown in Figure 3, open boundaries exist at the offshore extents of the model domain and require the 

specification of boundary conditions that drive the tidal flows through the model area. For the present 

study, a time varying water level derived from astronomical tidal constituents for Scripps Pier was applied 

along the entire offshore model boundary with no phase or amplitude adjustment made. 

3.3.2.4 Source/Sink 

In order to account for flows in and out of the nearby power plant, a source-sink was included in the 

model. A constant recirculating flow was applied at intake and outfalls of the power plant equaling 17.5 

m3

/s or approximately 400 million gallons per day (MGD). This value was selected as representative of 

typical power plant operating conditions at the time that desalinization would occur (winter season), 

based on data from Jenkins and Wasyl (1996). Historical flow rates vary between approximately 50 and 

600 mgd, with most flow fluctuations occurring in the summer and early fall months. Any differences in 

flow rates from those used in this study may affect the local salinity distributions near the power plant 

intake and outfall. For example, if actual flow rates during desalinization are larger than those used here, 

higher salinity waters may extend closer to the intake and further from the outfall. Also, high velocities 

associated with large outfall flow rates will influence local mixing and stratification is likely to be short 

lived. 

3.3.3 Salinity Transport Modeling

3.3.3.1 Overview and Discussion 

The salinity transport modeling was performed using the MIKE 21 NAD (Nested Advection-Dispersion) 

model running together with the MIKE 21 NHD model, and coupled to the MIKE 11 model of Otay 

River. For reasons of time and budget constraints, a rigorous salinity calibration was not performed. 

Instead, DHI relied upon experience in similar environments to select model parameters (dispersion 

coefficients) related to salinity transport and mixing. 

. 
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3.3.3.2 Dispersion Coefficients 

Dispersion coefficients are the main parameters specified in the salinity model. Selection of dispersion 

coefficients can be a difficult process, and requires detailed measurements. Instead of carrying out a 

comprehensive calibration procedure, the dispersion coefficients applied in the present study have been 

selected based on the assumption that the dispersion coefficients are dependent upon the grid spacing and 

time step of the model. The dispersion coefficients have been estimated through the relation: 

/ ∆∆•= txKD 2

where D is the dispersion coefficient, K is a proportionality constant, ∆x is the grid spacing, and ∆t is the 

computational time step. Based on our experience in similar systems, the constant K typically ranges from 

approximately 0.01 to 0.06. We selected a value of 0.02 for this study as the typical mid-range value from 

experiments, and has been found to provide reasonable mixing characteristics in similar model studies. 

From this relation above, the dispersion coefficients used in the modeling were: 

 

D = 22.5 m2

/s (75 m grid) 

D = 2.5 m2

/s (25 m grid) 

3.4 MODEL VALIDATION 

Results from the hydrodynamic model were compared to measured water levels and currents around the 

Bay. Measurements of water level and currents were available from various sources, and data collected by 

NOAA/USGS/US Navy from 1983 were used. 

3.4.1 Water Level Validation

For the validation period, three tide level gauges were available for comparing against model predictions. 

Figure 6 shows the locations of these stations (SSD, SD, and BP). The time period used for the water 

level measurement validation was 9/6/83 to 10/6/83.1

 Table 3-3 compares the modeled versus measured 

tidal constituents for the main 4 constituents that represent the bulk of the tidal forcing due to the 

attraction of the moon and sun on surface waters of Earth. For mixed tides such as those in San Diego, 

the main semi-diurnal tidal constituents are M2 (principal lunar) and S2 (principal solar), and the main 

diurnal forcing from the K1 (luni-solar declination), 01 (principal lunar) constituents. The constituent 

harmonic analysis is based on a least squares method, using DHI’s tidal analysis package (Foreman, 1977 

and DHI, 2001). The results of the constituent analysis indicate that modeled water levels match well 

with measured water levels throughout San Diego Bay. 

 

1

 The effects of sea level rise since 1983 are small and are expected to be within the range of error of the modeling. 
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3.4.2 Current Validation

For the validation period in 1983, eight mechanical current meters were identified as useable for 

comparing against model predicted currents. Figure 6 shows the locations of these current meter stations. 

The time period used for the water level measurement calibration was 9/6/83 to 10/6/83. Table 3-4 

compares the modeled versus measured tidal current constituents for the main tidal constituent, M2. The 

constituent analysis is based on a least squares method as previously described in Section 3.4.1. 

Generally the comparison is quite good. Discrepancies are most likely attributable to the fact that there 

were reportedly some problems with the mechanical meters, and the fact that these point measurements 

may not be representative of depth-averaged conditions simulated by the model. 
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Table 3-3. Comparison of Modeled Versus Measured Water Levels Tidal Constituents 

M2 K1 O1 S2 

Results Amp Phase Amp Phase Amp Phase Amp Phase 

(cm) (deg) (cm) (deg) (cm) (deg) (cm) (deg) 

Tides at Ballast Point (BP) 

Model 51.7 271.8 33.2 86.4 20.5 81.2 20.7 258.2 

Field Data 51.6 270.1 33.6 87.3 21.9 81.2 20.4 256.2 

Difference 0.1 1.7 -0.4 -0.81 -1.4 -0.0 -0.3 2.0 

Tides Downtown (SD) 

Model 54.4 273.6 33.5 87.4 20.7 82.3 21.9 260.2 

Field Data 54.0 271.7 33.7 87.8 21.4 80.8 22.4 260.5 

Difference 0.4 1.8 -0.2 -0.4 -0.7 1.5 -0.4 -0.4 

Tides at South San Diego Bay (SSD) 

Model 57.3 276.6 33.9 89.0 21.0 84.1 23.2 263.8 

Field Data* 57.0 273.9 34.5 87.8 21.6 82.0 24.0 264.2 

Difference 0.3 2.6 -0.6 1.2 -0.5 2.0 -0.8 -0.4 

*

Field data available only from 1993 and analysis performed on this data. 

Field data constituents reprinted from Wang, et al. (1998) 

Table 3-4. Comparison of Modeled Versus Measured Current Speed, for Tidal Constituent M2 

Model Results, 1983 From Measurements, 1983 

Major Minor Inclination Phase Major Minor Inclination Phase 

Station 

(m/s) (m/s) (deg) (deg) (m/s) (m/s) (deg) (deg) 

Constituent M2 

N1 0.085 0.004 92.1 247.8 0.102 0.009 91.6 258.3 

N2 0.063 -0.001 86.9 242.9 0.097 0.000 92.9 263.3 

N4 0.121 0.002 86.1 242.1 0.106 -0.008 94.3 224.0 

N5 0.171 0.0000 134.0 253.2 0.167 0.010 135.7 246.7 

N8 0.387 -0.001 128.8 250.4 0.325 0.018 136.4 238.9 

N10 0.233 0.001 26.1 67.4 0.265 0.005 27.1 59.0 

N12 0.201 0.000 167.9 250.4 0.179 -0.015 163.0 244.0 

N13 0.213 0.000 133.8 249.4 0.206 -0.005 139.3 246.0 

Note: Inclination is the direction of the major axis of tidal current ellipse, in degrees and counterclockwise from x-axis (east-west 

axis). Major/minor is the speed of the dominant/weaker tidal current. Phase is a measure of the relative time reference
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4. SALINITY REDUCTION MODELING 

4.1 INTRODUCTION 

The linked 1D-2D model described in Section 3 was applied to simulate tidal hydrodynamics and salinity 

transport within the Bay, ponds, and lower Otay River. In particular, the modeling effort assessed 

changes in pond and Bay salinities that would result from breaching salt pond levees for salinity 

reduction. This approach to salinity reductions relies on tidal mixing through the breaches to flush 

hypersaline water from the ponds. We modeled phased salinity reduction for Alternatives C4 and D, per 

discussions with DU and USFWS. 

Results from the modeling effort are presented in two forms. Contour maps of salinity in the ponds and 

south San Diego Bay at various stages after breaching were generated in order to illustrate the magnitude 

and extents (spatial and temporal) of increases in Bay salinities. Since these contour plots show only 

“snapshots” at particular times, we also present continuous time series of salinities in the Bay and ponds 

for selected locations over the simulation periods. 

Although no precise discharge criterion has been established for release of saline waters to the Bay, 

increases of 5 ppt above ambient conditions were selected as an initial target level. Prior to project 

implementation, acceptable discharge criteria will need to be selected in conjunction with regulatory 

agencies such as the Regional Water Quality Control Board and will need to consider impacts to species 

and existing ecology. Salinity levels in San Diego Bay can be quite variable. Surface salinities in San 

Diego Bay were monitored during a five-year fish study conducted between July 1994 and April 1999 

(Allen 1999). Salinities in the bay were generally higher than in the ocean, with bay-wide average 

salinities ranging from 32 ppt to 39 ppt during the course of the study. Salinities were generally highest 

in October and in the south bay, where they reached highs of 40 ppt in October 1996. 

4.2 ALTERNATIVES CONFIGURATION 

The configurations of Alternative C Option 4 and Alternative D are shown in Figure 1 and Figure 2. We 

modeled phased salinity reduction for Alternatives C4 and D, per our discussion with DU and USFWS. 

For both alternatives, Phase 1 consists of desalinization of Ponds 10, 10A, and 11. Desalinization may 

occur through breaching or by routing the water from the Phase 1 ponds into other ponds. We assume that 

the Phase 1 ponds would be tidal and at ambient salinities (approximately 33 ppt) prior to initiating Phase 

2. In Phase 2, Ponds 12-15 would be breached. Alternative D includes an additional third phase, in 

which Ponds 23-25 and 28-30 are breached once salinities in the Phase 2 ponds have reached ambient 

levels. In each phase, ponds breached and desalinated in previous phases were modeled as tidally active 

and at ambient salinity levels. 

Because of the limited number of model runs contracted, we modeled only salinity reduction for Phases 2 

and 3 in this study. Pond desalinization in Phase 1 is expected to occur more quickly and with fewer 
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salinity effects to the Bay than in Phases 2 and 3 because of the lower salinities and total mass of salt in 

the Phase 1 ponds (see Table 4-1 for pond salinities). 

We used the existing pond topographies from DU, modified to include the proposed supra-tidal nesting 

areas, as shown in Figures 1 and 2. Pond topographies were not modified to include final grading (cuts 

and fills) for cordgrass and tidal marsh creation, per instruction from DU (S. Carroll, pers. comm.). 

Therefore, we assume for this study that any grading would occur after desalinization. The exception is 

the inclusion of the nesting fills, which were incorporated into the model before the decision to maintain 

the existing pond grades had been made and these remained in the model. These fills do not significantly 

change the results or conclusions of this study. 

We selected initial pond salinities and water levels representative of late September to mid-February 

conditions. Pond breaching would be conducted during this time of year to avoid impacts during the 

nesting season. Therefore, initial salinities were calculated by taking the average of measured salinities 

occurring between September and mid-February. The seasonally-averaged salinities are given in Table 

4-1. Ambient salinity was assumed to be 33 ppt and was applied uniformly over the ocean, the bay and 

the Otay River for initial model startup. Water surface elevations were provided by DU and are shown in 

Table 4-1. 

Salinity reduction was simulated over a two month period, using measured tide data from 9/4/1983 to 

11/6/1983 to drive the model at the offshore boundaries. The hydrodynamic model was allowed to spinup for two days prior to breaching the ponds, which occurred at slack high water during the peak of the 

spring tide cycle. Pond breaches were modeled as broad-crested weirs with crest elevations of time 

varying crest elevations which start at a high elevation (closed) and drop to the existing elevations of the 

pond bed at each location. The breaching process (lowering of the weir crest) was scaled over a 6-hour 

period. This scaling represents the time over which the breaches would be constructed and prevents model 

instabilities associated with sudden changes in system bathymetry. 

For Phase 2, we used breach widths of 5 meters on all the ponds. A 5-meter width was found to provide a 

good balance between being large enough for rapid desalinization of the ponds, yet small enough to 

reduce the spike in bay salinities immediately after breaching. Breach widths of 10 meters, 15 meters, and 

2.5 meters were also tested at a cursory level. Results from the 10- and 15-meter runs indicated a larger 

spike in the bay salinities immediately after breaching, but with no significant benefits in terms of more 

rapid desalinization times. Results from the 2.5-meter breach did not reduce these short-term impacts in 

the bay appreciably beyond those simulated by 5 meter breaches. A 5 meter breach width exhibits slight 

tidal damping compared to 10 meters width which was found to provide full tidal exchange with no 

damping. For Phase 3, we assume that 5-meter breaches connect the Phase 3 Ponds (Ponds 23, 24, 25, 

28, 29 and 30) to Ponds 13 and 15. Breaches from the Phase 2 Ponds to San Diego Bay are assumed to 

have enlarged to widths of 10 meter in response to tidal action. 

Breach sizes were selected for salinity reduction only. Breach locations were provided by USFWS and 

DU (Figures 1 and 2). Final breach sizing and locations will be based on habitat restoration objectives 
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(e.g., full tidal exchange in the short and long-term, channel shape similar to natural channels), and will 

likely differ from those used here. 

Table 4-1. Initial Conditions: Pond Water Surface Elevations and Salinities Prior to Breaching 

POND 

NUMBER 

Elevation 

(ft, NAVD)

Elevation

(m,NAVD) 

Elevation

(m,msl) 

Salinity (ppt) 

Phase 1 Ponds 

10 5.8 1.77 1.06 33* 

10A 5.8 1.77 1.06 33* 

11 5.8 1.77 1.06 33* 

Phase 2 Ponds 

12 5.5 1.68 0.97 61.0 

13 5.2 1.58 0.88 76.7 

14 5.2 1.58 0.88 90.7 

15 5.0 1.52 0.82 92.6 

Phase 3 Ponds 

20 11.4 3.47 2.77 111.5 

21 11 3.35 2.65 114.7 

22 8.5 2.59 1.89 142.8 

23 8.4 2.56 1.86 214.3 

24 8.3 2.53 1.83 262.4 

25 8.2 2.50 1.80 268.0 

28 7.0 2.13 1.43 281.0 

29 9.3 2.83 2.13 290.4 

L 7.0 2.13 1.43 NA 

30 9.1 2.77 2.07 278.0 

* Assume already breached in Phase 1 and restored to ambient salinities. 

4.3 RESULTS 

4.3.1 Phase 2

4.3.1.1 Salinity Reduction in the Ponds 

Figure 7 shows a time series plot of the salinity variation inside the Phase 2 ponds. Note that the salinity 

values are averaged over the entire pond volume. Figure 8 through Figure 10 show the depth-averaged 
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instantaneous salinity fields of the ponds at selected periods for 1 day, 7 days and 28 days after breaching, 

both at low and high tides. 

Ponds 12, 14 and 15 reduce in salinity to nearly equal levels fairly rapidly, and after approximately 7 days 

have dropped below 38 ppt or 5 ppt above ambient levels. After 1 month they have reduced to about 35 

ppt, or 2 ppt above ambient levels. Salinity reduction in Pond 13 is slightly slower due to the fact that it 

is not directly breached to the bay, and relies on tidal action in Pond 12 for flushing power during Phase 

2. Also, the bed elevation of Pond 13 is higher in the tide frame and much of the pond is dry during low 

tide, which reduces the overall mixing capacity of the pond. Pond 13 is reduced to 38 ppt after 24 days. 

4.3.1.2 Salinity Increases in San Diego Bay 

Figure 8 through Figure 10 show the depth-averaged instantaneous salinity fields of the lower South Bay 

at selected periods for 1 day, 7 days and 28 days after breaching, both at low and high tides. Salinities at 

various locations in San Diego Bay (shown in Figure 11) are plotted as time series in Figure 12. The plots 

show that salinity impacts are most significant near the ponds, and are fairly well reduced by the time the 

plume reaches Location C. Salinities at all locations are significantly reduced and approach ambient 

conditions by 28 days. 

4.3.2 Phase 3

4.3.2.1 Salinity Reduction in the Ponds 

The existing elevations in the Phase 3 Ponds, as shown in Figure 5, are above mean tide level (MTL), 

with a majority above mean higher high water (MHHW). Due to the existing topography, these ponds are 

rarely tidal, except for ponds 25 and 28 which are partially tidal. Although these high-elevation ponds do 

not drain completely due to the micro topography of the bed surface, most of the water is discharged over 

just 6 hours, which corresponds to the duration of the first ebb tide. Therefore, salinity reduction in Phase 

3 Ponds is very short, expect for localized areas where the hypersaline water is not able to completely 

drain. 

4.3.2.2 Salinity Increases in San Diego Bay 

Figure 13 through Figure 15 show near-field impacts to San Diego Bay 1, 7, and 28 days after breaching 

of the Phase 3 ponds at corresponding low and high tides. After 1 day, the greatest impacts to the bay 

salinity are mostly contained to the south of the power plant causeway, and are about 40 ppt above 

background levels. Note that salinities in the Phase 2 Ponds are even higher, and act to dampen the shortterm impacts to the bay. After 7 days, the impacts north of the causeway are less than 5 ppt above 

background. Numerical results indicate that after 28 days, impacts to the bay are negligible. 

Figure 16 plots time series of salinities at the points throughout the bay shown in Figure 11. Although 

these results are qualitatively similar to the far-field impacts for Phase 2, bay salinities following 

discharges from the Phase 3 Ponds are much higher. The results presented in Figure 16 show that salinity 
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impacts are most significant near the ponds, and are fairly well reduced by the time the plume reaches 

Location C. Additionally, the impacts are only appreciable in the short-term, with bay salinities dropping 

to below the +5 ppt threshold shortly after 7 days. 

4.4 MODEL LIMITATIONS AND MANAGEMENT CONSIDERATIONS 

Application of the numerical model was useful in quickly developing estimates of flushing time in the 

ponds as well as increases in Bay salinities. However, the following items should be considering when 

interpreting the numerical results: 

• The model provides estimates of the magnitudes and time scales of salinity impacts to the 

bay, and provides a basis for comparison between alternatives that is appropriate for 

preliminary feasibility assessment. It can be used to screen various salinity reduction 

alternatives. If the breaching salinity reduction alternative is carried forward in project 

planning, we recommend that the model be refined. This approach of using an initial 

screening level model and subsequent refinement was used in planning for the Napa Salt 

Marsh Restoration Project. Refinements would include additional calibration, validation, 

and sensitivity assessment, plus additional details of the restoration plan once these are 

developed. A more thorough calibration, validation, and sensitivity assessment would help 

to define and narrow the uncertainties in the modeled results. 

• If more a refined analysis is required for alternative analysis during later stages of the 

planning effort, we recommend re-visiting the selection of the dispersion with a more 

complete dataset of measured salinity. This would reduce uncertainties associated with the 

incomplete calibration. Salinity measurements needed for a complete calibration of the 

advection-dispersion model were not available within the time frame dictated by the project 

schedule, and we relied on our experience with similar systems to construct the model. The 

choice of dispersion coefficient affects the size and magnitude of salinities in the bay. Large 

values of the dispersion coefficient will increase the spatial extent and lessen the magnitude 

of salinity increases (mass of salt is conserved). The converse is true for small values of the 

dispersion coefficient. The results of desalinating the ponds probably are not that sensitive to 

changes in dispersion coefficients, since the flushing of these ponds is driven by advection 

processes and due to the breach size and bed elevation of the ponds relative to the tide range. 

• Breach sizes and locations are preliminary, and are expected to be refined based on habitat 

objectives later in project design (Section 4.2). Breach timing is also preliminary and may be 

refined based on detailed consideration of construction feasibility. Simultaneous breaching 

was assumed in the salinity reduction alternatives, resulting in hypersaline discharges from 

multiple ponds at the same time. Management of the actual salinity reduction program may 

include staggering the levee breaches so that tidal action is restored to the ponds one at a 

time. This would lessen the magnitude of salinity increases in the Bay, but extend salinity 

reduction of the complex. Adaptive management of the desalination program for the 
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complex could be aided by monitoring salinity levels in South San Diego Bay to reduce the 

possibility of unanticipated adverse impacts to wildlife. 

• The modeling assumes a certain set of initial pond salinity and water level conditions. The 

plan will need to include sufficient flexibility for actual conditions that vary annually. 

• Application of the 2D MIKE model should be limited to systems without appreciable 

stratification. According to the literature (Wang et al 1998), San Diego Bay can be treated as 

well mixed, except during infrequent periods of freshwater inflow from the Sweetwater and 

Otay rivers. These rare stratifications could persist for a few days during low tide energy 

periods (neap tides). Stratification may also occur when warm water discharges from the 

South Bay power plant flow over more dense saline Bay water. The effect of this 

stratification on salinities would be strongest near the power plant discharge, although large 

velocities at the outfall wound tend to mix effluent throughout the water column. During 

desalination of the salt ponds, stratification may also develop if density differences between 

the effluent and receiving water outweigh the vertical mixing in the Bay. Therefore, the 

Estuarine Richardson Number (Fischer 1979) was computed using modeled results to asses 

the likelihood of stratification due to salinity reduction. This non-dimensional number is a 

measure of the stabilizing power of density differences to the mixing power in the Bay. The 

computed Richardson number is at the lower end of the range at which strongly stratified 

flow could be expected, suggesting that the depth-averaged model is appropriate for this level 

of analysis. Additionally, wind-waves were not included in the numerical model and would 

increase the vertical mixing in the shallow portions of South San Diego Bay. 

• Dissolution of precipitated salts was not taken into account in the present modeling exercise, 

and may affect the time required to reduce pond salinities to ambient levels. However, we do 

not expect the dissolution process to significantly affect the short-term changes in Bay and 

pond salinities presented above. Uptake of precipitated salts and salinity in the underlying 

soils is likely a rate-limited process, with time scales longer than the flood-ebb tidal cycle. 
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5. BRINE FEASIBILITY 

Alternative D contains a brine management component, shown in Figure 2. Brine ponds would be 

managed to create habitat for brine shrimp and brine flies, and foraging areas for waterfowl and 

shorebirds. PWA created a simple box model to assess the feasibility of maintaining the proposed brine 

operation in terms of the flow rates required to maintain suitable habitat in the ponds and to dilute the 

hypersaline brine prior to discharge to the Bay. This analysis was carried out at a conceptual level. No 

numerical modeling was performed in this initial assessment. 

5.1 CONFIGURATION OF THE BRINE COMPLEX 

As shown in Figure 2, the brine complex is located at the easternmost extents of the project area, and 

includes Ponds 42, 43, 45, 46, and 47. To ensure proper habitat for brine shrimp and brine flies, the target 

salinities in the brine ponds range between 80 and 120 ppt. Per our discussions with the planning team, 

we assume that new hydraulic structures would be installed to convey the required water and that pumps 

would be used as necessary to move water through the system. A preliminary criteria for release of water 

into San Diego Bay was +5 ppt. As per the salinity reduction discussion in Section 4, actual discharge 

criteria for the project will need to be agreed upon between the project sponsors and relevant agencies. 

A number of management scenarios are possible for the brine complex. A source of inflow to the brine 

ponds is required to offset evaporation and maintain suitable conditions in the ponds. Due to the elevated 

salinity in the brine complex, discharges from these ponds must be diluted prior to release into San Diego 

Bay. The basic components of brine management are: a source of inflow to the brine ponds; a source of 

water, referred to as make-up water, to dilute the brine pond outflow; a mixing basin in which to combine 

the brine outflow and make-up water; and discharge to the Bay. 

The assumed route for flows through the brine ponds is shown in Figure 17. We assumed that inflow to 

the brine ponds would be supplied from the managed ponds, since this water would already be at slightly 

elevated salinity levels and it makes more sense to route it to the brine ponds rather than discharging it to 

the Bay. Based on our experience with ponds managed for water fowl and shorebird habitat at the Napa 

River salt ponds in San Francisco Bay, we assumed that these managed ponds would have salinities of 

approximately 40 ppt. Several ponds would be suitable as mixing basins. We considered Ponds 41 and 

48, since they are adjacent to the brine ponds. Pond 41 is shown as the mixing basin in Figure 17. Makeup water to the mixing basin is assumed to come from Bay water. This could be supplied from any of the 

tidal ponds, preferably as far from the eventual brine discharge point as possible. Salinities in the mixing 

basin would be maintained at ambient salinity +5 ppt. The diluted effluent could then be discharged into 

the canal west of Ponds 41 and 30. If pond 48 is used as the mixing basin, some grading and levee 

construction would be required to connect Pond 48 with the canal. 
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5.2 THE BOX MODEL 

PWA developed an analytical mass-balance model to track salinity and water volumes in the brine 

complex and mixing basin. The brine ponds were considered one unit in order to simplify the analysis. 

Figure 18 shows a schematic of the box model structure. A mass balance of salt and water is applied to 

the brine complex, which receives inflow at 40 ppt from the managed ponds and discharges to the mixing 

basin. A second mass balance is applied to the mixing basin, which uses make-up water from the Bay to 

dilute the hypersaline (80 – 120 ppt) discharges from the brine ponds. Make-up water for the mixing 

basin is assumed to come from the Bay or tidal ponds at 34 ppt2

, and, as noted above, salinity in the 

mixing basin is limited to 39 ppt. Both the brine ponds and mixing basin are subject to freshwater losses 

and gains due to evaporation and precipitation. 

Mean monthly rates of evaporation and precipitation were collected from readily available sources. 

Published mean monthly data collected by the National Weather Service (NWS 2002) at Chula Vista 

from 1960 – 1990 were used to establish typical rates of precipitation. Evaporation rates were determined 

based on data from the California Department of Water Resources (DWR). As shown in Figure 19, 

evaporation barely outpaces precipitation during the winter but is much more intense in the summer. 

Essentially, it is the net evaporation, along with the flow rates through the system, which determine the 

salinity and water volumes in the ponds. 

The simplicity of the box model allowed PWA to quickly screen various configurations and management 

scenarios at a cursory level. Table 5-1 summarizes the model set up for each of the five screening runs 

analyzed by PWA. Based on the results of the screening runs (Table 3-1), we selected Run 4 for further 

consideration. Run 4 consisted of prescribing an intake flow rate from the managed ponds into the brine 

complex (QIN), and using the box model to estimate the resulting salinity. Management of the brine 

complex was then optimized by minimizing the peak summer pumping rate (QIN) while keeping the brine 

ponds in their target salinity range (80 – 120 ppt). The box model was then applied to calculate the makeup flow rate (QMUP) required to maintain the mixing basin at a constant 39 ppt. The intake and make-up 

flows were seasonally-varied in order to stay within the range of target brine salinities and were optimized 

within the constraints of the configuration to reduce the peak summer pumping rates. 

5.3 RESULTS 

Results for Run 4 are discussed below. 

 

2

 Ambient salinity levels for the brine analysis were assumed to be 34 ppt since make-up water will be drawn from 

the southernmost reach of the Bay. Measurements from the Port of San Diego show seasonally-averaged salinities 

in this area to be slightly higher than the central and northern sections of the Bay. 

(Data source: http://www.portofsandiego.org/sandiego_environment/bay_water_sampling.asp) 
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5.3.1 Brine Ponds

Results from the brine complex are shown in Figure 20, which plots the flow rates and salinity through 

these ponds. The results show that, under typical metrological conditions, the brine ponds delineated in 

Alternative D can be maintained between 80 – 120 ppt with modest pumping rates. Pumping into the 

brine ponds varies from approximately 60 gpm in the winter to 170 gpm during the summer months. 

Peak salinity levels in the ponds lag the peak pumping by about three months, with the highest salinities 

(approximately 120 ppt) occurring in late autumn. During the late winter and early spring months, 

salinity in the brine ponds drops to 80 ppt. Peak salinities lag peak pumping rates by three months 

because of evaporation and the pumping strategy employed in the model. The pumping strategy shown in 

Figure 20 was to “prime” the brine ponds by reducing their salinity early in the summer, when it was 

relatively easy to outpace evaporation. Then during the summer, the brine ponds are not near the upperlimit of acceptable salinity and can accommodate increases in salinity. If salinities were not “primed” 

(i.e., lowered) at the beginning of the summer, it would be more difficult to outpace intense summer 

evaporation, there would be less management flexibility, and peak pumping rates would probably be 

higher. 

Water levels in the brine ponds varies seasonally and, for the configuration modeled, levee improvements 

may be required to prevent overtopping in Pond 42. A uniform water surface elevation was assumed 

across the brine ponds and average bed elevations were used to convert the water volume computed by 

the box model to the depths plotted in Figure 21. Water levels in the brine ponds are inversely related to 

salinity, with a maximum depth in mid-March and minimum in late autumn. It may be possible to avoid 

levee improvements, using different brine pond management strategies. For example, it may be possible 

to limit water levels in Pond 42, but allow higher water levels elsewhere in the brine complex. 

5.3.2 Mixing Basin

As described above, the box model was applied to Pond 41 to estimate how much make-up water is 

required to maintain the mixing basin (Pond 41) at 5 ppt above ambient levels for the brine discharges 

plotted in Figure 20. As shown in Figure 22, the flow rate of make-up water into the mixing basin peaks 

at about 1330 gpm. Approximately 900 gpm (68 % of the total) is needed to dilute the brine effluent to 

discharge levels, and the remaining 420 gpm (32 % of the total) is required to offset the effects of 

evaporation within the mixing basin. These results suggest that the required pumping rates are feasible, 

assuming continuous pumping. Discharges to the Bay range between 330 and 1330 gpm (Figure 22). 

The pumping rates could be reduced by diluting the brine discharges with flash mixing, in which brine 

outflow is rapidly diluted in a small basin or canal prior to discharge to the Bay. Flash mixing requires 

smaller flow rates since the effects of evaporation on a small pond surface area are negligible. Flash 

mixing reduces peak flows to approximately 800 gpm (from 1330 gpm). Make-up flows with flash 

mixing are shown as the green line in Figure 22. The canal west of Ponds 30 and 41 provides a possible 

location for flash mixing. An alternative solution may include a passively-managed, gravity-driven 

system that relies on tidal flushing. Such a system, however, would require grading (excavation) of Pond 

41 since its bed elevation is currently above high water levels (see Figure 5). 
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The resulting flushing time3

 varies from approximately 10 days when the make-up flow rate is maximum, 

to about 37 days during periods of low flow (Figure 23). Flushing times greater than a month may lead to 

deteriorated water quality, and the low pumping rates during these periods could be increased to alleviate 

these concerns. 

5.4 MODEL LIMITATIONS AND MANAGEMENT CONSIDERATIONS 

The box model suggests that management for brine habitat is feasible from a physical processes 

perspective. The box model includes several simplifying assumptions for the purpose of preliminary 

feasibility assessment. If the brine management component is carried forward in project planning, these 

assumptions will need to be assessed in more detail later in the planning and design process. In addition, 

further analysis could be useful for identifying lower cost implementation approaches, particularly to 

reduce the cost of pumping. 

Brine operations should include flexibility in management of flows. Management considerations include: 

pond drying or levee overtopping, climatic variations (discussed further below), maintaining brine 

salinities within the target range for habitat, potential for gypsum formation if salinities exceed 

approximately 150 ppt, water quality in the ponds, and potential for temporary pump failure. 

The box model considers the brine ponds as one large, well-mixed pond with uniform water levels. In 

reality, salinities and water levels will vary between the ponds, with the extent of variation dependent on 

the exact pond configuration. 

The model assumes average monthly rainfall and evaporation conditions. Daily and annual (wet and dry 

year) variations will affect the amount of pumping required for brine management and dilution. These 

variations could also affect brine salinities and the potential for pond drying and levee overtopping. Brine 

management scenarios for wet and dry years should be considered during future planning stages prior. 

The modeled brine configuration assumes a seasonal-varying supply of 40 ppt water from the managed 

ponds. Managed pond operations have not been modeled and we did not evaluate the feasibility of 

meeting the assumed inflows to the brine ponds. However, given the high evaporation rates in South San 

Diego Bay, it is likely that a significant amount of flow through the managed ponds will be required to 

maintain suitable salinities in those ponds. Additionally, it would be possible to meet the brine pond 

target salinities even if Bay water (at approximately 34 ppt) were needed to augment the inflow from the 

managed ponds. This would affect flow rates in the brine pond and mixing basin flow, as well as 

residence times. Operations for the brine complex will need to be coordinated with those for the managed 

ponds in later project planning. 

Intake and make-up flows were fit to the shape of a sine wave for ease in modeling seasonal variations. 

 

3

 Flushing Time = Pond 41 Volume / Make-up Flow Rate = V / QMUP
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In reality, brine operations are likely to use stepped or discontinuous flow/pumping rates. Therefore, 

actual operations may require higher pumping rates than those modeled here. For stepped pumping, 

differences from the peak modeled flows are expected to be minor. For discontinuous pumping, peak flow 

rates will be several times the modeled rates, but still within the range of typical pumping operations (e.g., 

pumping one day out of seven yields increases peak flow rates from 2.9 to 20 cfs). More detailed brine 

runs could be conducted to optimize the pumping rates. Additional cost reduction may be possible by 

modifying the management configuration to use gravity-driven flows for brine inflow and/or dilution. 
DRAFT 

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Table 5-1. Run Catalog for Box Model 

Brine Complex Mixing Basin 

Volume Salinity Intake Flow Pond Volume Salinity Make-up 

Flow 

Run 1. Constant brine salinity 

Prescribe as constant 

Constant (100 ppt) 

Calculated 48 Constant Constant 

(39 ppt) 

Calculated Flow into th

mixing basin1200 gpm, r

Run 2. Constant brine intake flow 

Calculated Calculated Prescribe as 

constant 

48 Constant Constant 

(39 ppt) 

Calculated Constant flo

110 gpm canwithin the tappt. 

Run 3. Varying brine salinity and intake flow 

Calculated Calculated Prescribe as 

time-varying 

48 Constant Constant 

(39 ppt) 

Calculated Flow into th

mixing basin 1036 gpm, rsalinity in 80 

Run 4. Same as Run 3, but with Pond 41 as mixing basin 

Calculated Calculated Prescribe as 

time-varying 

41 Constant Constant 

(39 ppt) 

Calculated Make-up flo

increases to surface area 

Run 5. Same as Run 4, but allowing mixing basin salinity and volume to vary 

Calculated Calculated Prescribe as 

time-varying 

41 Calculated Calculated Prescribe as 

time-varying 

Make-up flo

Note: “Calculated” means that this parameter was determined from the box model. 
 

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6. LIST OF PREPARERS 

This report was prepared by the following PWA staff: 

Michelle Orr, Project Manager 

Don Danmeier, Assistant Project Manager 

Jeff Haltiner, Project Director 

Chris Campbell, Hydrologist 

 

With: 

Dale Kerper, DHI Water & Environment 
 

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7. REFERENCES 

Allen, Larry G. 1999. Fisheries Inventory and Utilization of San Diego Bay, San Diego California. 

DHI, 2001. "User Guide and Reference Manual, Tidal Analysis and Predictions". 

DHI, 2002. "MIKE 21 Environmental Hydraulics, Advection-Dispersion Module Reference Manual”. 

 

Fischer, et al., Mixing in Inland and Coastal Waters, Academic Press, Inc., N.Y. 1979. 

 

Foreman, M.G.G., 1977. "Manual for Tidal Currents Analysis and Prediction." Pacific Maine Science 

Report 78-6, Institute of Ocean Sciences, Patricia Bay, Sidney, B.C. 

Jenkins, S.A. and J. Wasyl, 1996. “Hydrodynamic Transport Study of Constituent Net Additions from 

the SDG&E South Bay Power Plant”. Report for SDG&E. August, 27, 1996. 

NWS, 2002. Website http://www.wrcc.dri.edu/cgi-bin/cliMAIN.pl?cachul_sca 

Tenera Environmental and Merkel and Associates, Inc., 2002. “Study Plans for 316(a) Thermal 

Discharge Assessment and 316(b) Resource Assessment”, For Duke Energy South Bay, LLC, October. 

Wang, P. F., R. T. Cheng, Kenneth Richter, E. S. Gross, Don Sutton, and J. W. Gartner, 1998. Modeling 

tidal hydrodynamics of San Diego Bay, California, Journal of the American Water Resources Assoc., 

Vol. 34, No. 5, p. 1123-1140. 

Western Salt Company, 1997. “South Bay Salt Making On the Chula Vista, California Plant”, March 

1997. 
 

FIGURES 

Figure 1 Configuration of Restoration Alternative C Option 4 

Figure 2 Configuration of Restoration Alternative D 

Figure 3 Extents of MIKE 21 Nested Model Grids 

Figure 4 Location of MIKE 11 Otay River and Breach Weirs 

Figure 5 Bed Elevations for Salt Ponds 

Figure 6 Locations of NOAA Current Measurements During the 1983 Measurement Period 

Figure 7 Pond Salinity Time Series, Phase 2 

Figure 8 Salinity Distribution in the South Bay and Ponds, Phase 2, 1 day after breach 

Figure 9 Salinity Distribution in the South Bay and Ponds, Phase 2, 7 days after breach 

Figure 10 Salinity Distribution in the South Bay and Ponds, Phase 2, 28 days after breach 

Figure 11 San Diego Bay Salinity Point Locations 

Figure 12 San Diego Bay Salinity Time Series, Phase 2 

Figure 13 Salinity Distribution in the South Bay and Ponds, Phase 3, 1 day after breach 

Figure 14 Salinity Distribution in the South Bay and Ponds, Phase 3, 7 days after breach 

Figure 15 Salinity Distribution in the South Bay and Ponds, Phase 3, 28 days after breach 

Figure 16 San Diego Bay Salinity Time Series, Phase 3 

Figure 17 Configuration of Brine Complex 

Figure 18 Conceptual Layout of Box Model 

Figure 19 Monthly Mean Evaporation and Precipitation Rates for Chula Vista 

Figure 20 Time Series of Discharges and Salinity in Brine Ponds 

Figure 21 Time Series of Brine Pond Water Depths 

Figure 22 Time Series of Mixing Basin Discharges 

Figure 23 Flushing Time in Mixing Basin 
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ALTLayout-Rev1.xls \fig1-AltC 

Source: USFWS

Sou

Configuration of Restoration 

PWA Ref 1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ALTLayout-Rev1.xls \fig2-AltD 

Source: USFWS

Sou

Configuration of Re

PWA Ref 1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ Fig3 4/11/2003

South San Diego Bay Salt Ponds

Extent of MIKE 21 Nested Model Grids

f i g u r e 3

PWA Ref 1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ Fig4 4/11/2003

South San Diego Bay Salt Ponds

Location of MIKE 11 Otay River and Breaches

fi g u r e 4

PWA Ref 1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ALTLayout-Rev1.xls \fig5Elevations 

Source: DTM from DU

Sou

Bed Ele

PWA Ref 1631

above MHH

W

MHW - MHHWMTL - MHWMLW - MTLMLLW - MLWbelow MLLW
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ Fig6 4/11/2003

Source: NOAA Measurements from 1983

South San Diego Bay Salt Ponds

Locations of NOAA Current Measurements

during the 1983 Measurement Period

f i g u r e 6

PWA Ref 1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ Fig7 

Notes: 

Salinities in Ponds are weighted average concentrations over the entire pond.Black bar represents ambient salinity (33 ppt).

Sou

Pond Salinit

PWA Ref 1631

30405060708090

100

9/6/1983 9/16/1983 9/26/1983 10/6/1983 10/16/1983 

BREACH

1 DAY

7 DAYS 28 DAYS
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ Fig8 4/11/2003

Notes: Simulated salinities at low and high tides, 

1 day after breach of Alternative C Option 4. South San Diego Bay Salt Ponds

Salinity Distribution in the South Bay & Ponds, 

Phase 2 , 1 Day After Breach

f i g u r e 8

PWA Ref 1631

Salinity 

Distribution in 

South San Diego 

Bay at high tide 

1 day after breach.

Salinity 

Distribution in 

South San Diego 

Bay at low tide 

1 day after breach.

INACTIVE 

PONDS

INACTIVE 

PONDS
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ fig9 4/11/2003

Notes: Simulated salinities at low and high tides,

7 days after breach of Alternative C Option 4. South San Diego Bay Salt Ponds

Salinity Distribution in the South Bay & Ponds

Phase 2 , 7 Days After Breach

f i g u r e 9

PWA Ref 1631

Salinity Distribution

in South San Diego 

Bay at high tide 

7 days after breach.

Salinity Distribution

in South San Diego 

Bay at low tide 

7 days after breach.

INACTIVE 

PONDS

INACTIVE 

PONDS
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ fig10 4/11/2003

Notes: Simulated salinities at low and high tides, 

28 days after breach of Alternative C Option 4. South San Diego Bay Salt Ponds

Salinity Distribution in the South Bay & Ponds, 

Phase 2 , 28 Days After Breach

f i g u r e 10

PWA Ref 1631

Salinity Distribution 

in South San Diego 

Bay at high tide 

28 days after breach.

Salinity Distribution 

in South San Diego 

Bay at low tide 

28 days after breach.

INACTIVE 

PONDS

INACTIVE 

PONDS
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ fig11 4/11/2003

South San Diego Bay Salt Ponds

San Diego Bay Salinity Point Locations - Alternative C Option 4

f i g u r e 11

PWA Ref 1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter3_and_4ALTC-rev.xls \ fig12 

3032343638404244464850

9/6/1983 9/16/1983 9/26/1983 10/6/1983 10/16/1983 

Salinity (psu)

BREACH

1 DAY

7 DAYS

28 DAYS

South S

San Diego Bay Salinit

PWA Ref 1631

Notes: See Figure 4.6 for location points A through 

G
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures\ Chapter4_ALTD-rev.xls \ fig13 4/11/2003

Notes: Simulated salinities at low and high 

tides, 1 day after breach of Alternative D. South San Diego Bay Salt Ponds

Salinity Distribution in the South Bay & Ponds,

Phase 3, 1 Day After Breach

PWA Ref 1631

Salinity 

Distribution in 

South San Diego 

Bay at high tide 

1 day after breach.

Salinity 

Distribution in 

South San Diego 

Bay at low tide 

1 day after breach.

INACTIVE 

PONDS

INACTIVE 

PONDS

f i g u r e 13
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures\ Chapter4_ALTD-rev.xls \ fig14 4/11/2003

Notes: Simulated salinities at low and high 

tides, 7 days after breach of Alternative D. South San Diego Bay Salt Ponds

Salinity Distribution in the South Bay & Ponds,

Phase 3, 7 Days After Breach

f i g u r e 14

PWA Ref 1631

Salinity 

Distribution in 

South San Diego 

Bay at high tide 

7 days after breach.

Salinity 

Distribution in 

South San Diego 

Bay at low tide 

7 days after breach.

INACTIVE 

PONDS

INACTIVE 

PONDS
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures\ Chapter4_ALTD-rev.xls \ fig 15 4/11/2003

Notes: Simulated salinities at low and high 

tides, 28 days after breach of Alternative D. South San Diego Bay Salt Ponds

Salinity Distribution in the South Bay & Ponds,

Phase 3, 28 Days After Breach

f i g u r e 15

PWA Ref 1631

Salinity Distribution 

in South San Diego 

Bay at high tide 

28 days after breach.

Salinity Distribution 

in South San Diego 

Bay at low tide 

28 days after 

breach.

INACTIVE 

PONDS

INACTIVE 

PONDS
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures\ Chapter4_ALTD-rev.xls \ fig16

30405060708090

100110120

9/6/1983 9/16/1983 9/26/1983 10/6/1983 10/16/1983 

Salinity (psu)

BREACH

1 DAY

7 DAYS

28 DAYS

South Sa

San Diego Bay Salinity Tim

PWA Ref 1631

Notes: See Figure 4.6 for location points A through G.
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ALTLayout-Rev1.xls \fig17Brine 4/11/2003

80 - 120

ppt

40

ppt

39

ppt

34

ppt

Source: Background image from USFWS (01 November 

2002)

South San Diego Bay Salt Ponds

Configuration of Brine Complex

f i g u r e 17

PWA Ref 1631

Flow Direction
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ALTLayout-Rev1.xls \fig18BrineConceptual 4/11/2003

40

ppt

34

ppt

South San Diego Bay Salt Ponds

Conceptual Layout of Box Model

f i g u r e 18

PWA Ref 1631

Brine Complex

80 - 120 ppt

Mixing Basin

39 ppt

Intake from managed ponds to 

brine complex at 40 ppt (QIN)

Discharge from brine complex to 

mixing basin for dilution (QOUT)

Make-up water introduced into 

mixing basin at 34 ppt (QMUP)

Discharge from mixing basin to 

San Diego Bay (QMIX) at 39 ppt

Evaporation (QE,B)

Precipitation 

(QP,B)

Precipitation (QP,M)

Evaporation (QE,M)
\Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ MeanEvap-chulaVista.xls \ fig19 

0.01.02.03.04.05.06.0

J FMAM J J A S O

Time

Rate (mm/day)

Effective EEvaporatiPrecipitati

South 

Monthly Mean Evaporation and Prec

Notes: Precipitation from 1961 to 1990; Freshwater evaporation from 1918 to 

1979 (values independently adjusted with Fullerton Class A pan coefficient)Source: National Weather Service (NWS)Cooperative Network - Chula Vista.

PWA Ref #1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter5-Brine.xls \ fig20 

20406080

100120140160180

J FMAM J J A S OND J FMAM J J A S O

Time

Discharge (gpm)

Qin Qout Brine Salinity

South 

Time Series of Discharges and Sal

Notes: Fit flows to a sine-wave and solve for time-varying volume and salinity ofbrine complex; set volume and salinity of mixing basin as constants and solve for time-varying flow (Run 4).

PWA Ref #1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter5-Brine.xls \ fig21 

0.00.51.01.52.02.53.03.5

J FMAM J J A S OND J FMAM J J A 

Time

Water Depth (ft)

South 

Time Series of Brine 

Notes: Fit flows to a sine-wave and solve for time-varying volume and salinity ofbrine complex; set volume and salinity of mixing basin as constants and solve for time-varying flow (Run 4)

POND 42

POND 43

POND 46

POND 47

POND 45

Dashed lines represent typical levee heights for each pond. Lines for Ponds 45 

PWA Ref #1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter5-Brine.xls \ fig22-rev 

0

200400600800

100012001400

J FMAM J J A S OND J FMAM J J A S 

Time

Discharge (gpm)

Qmup - Total Q - dilute Brine Disc

South 

Time Series of Mixin

Notes: Fit flows to a sine-wave and solve for time-varying volume and salinity of 

brine complex; set volume and salinity of mixing basin as constants and solve for time-varying flow (Run 4). Discharge into the bay is = Qmup-total (blue line) + Qout (red line) - Pond 41 Evap.

Flow required to dilute b

effluent to +5 ppt

Effects of 

evaporation 

in Pond 41

PWA Ref #1631
Projects\1631-00_San_Diego_Salt_Ponds\Task6-Reporting\figures \ Chapter5-Brine.xls \ fig23 

0

200400600800

100012001400

J FMAM J J A S OND J FMAM J J A S 

Time

Discharge (gpm)

Qmup (Pond 41) Flushing Time

South 

Flushing Tim

Notes: Fit flows to a sine-wave and solve for time-varying volume and salinity of 

brine complex; set volume and salinity of mixing basin as constants and solve for time-varying flow (Run 4)

PWA Ref #1631
 

Appendix K 

Compatibility Determinations 
Compatibility Determinations 

Appendix K includes the following draft compatibility determinations: 

Sweetwater Marsh Unit

Wildlife Observation and Photography 

Environmental Education and Interpretation 

Mosquito Management 

Fishing 

Water Trail 

South San Diego Bay Unit

Wildlife Observation and Photography 

Environmental Education and Interpretation 

Mosquito Management 

Regional Trail 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 1 of 7 

Compatibility Determination

-FINALUse: Wildlife Observation and Photography 

Refuge Name: Sweetwater Marsh Unit of the San Diego Bay National Wildlife Refuge 

 (San Diego County, Cities of Chula Vista and National City, California) 

 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the Sweetwater Marsh Unit are the Endangered 

Species Act of 1973, as amended (16 U.S.C. §§1531-1543); Fish and Wildlife Act of 1956, 

as amended (16 U.S.C. §§742a-742j, not including 742d-742l); and the Fish and Wildlife 

Coordination Act of 1934, as amended (16 U.S.C. §§661-667e). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge (NWR) was established: 

“to protect, manage, and restore habitats for federally listed endangered and 

threatened species and migratory birds, and to maintain and enhance the biological 

diversity of native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species 

Act of 1973, as amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as 

amended); 

”...for the development, advancement, management, conservation, and protection of 

fish and wildlife resources...for the benefit of the United States Fish and Wildlife 

Service, in performing its activities and services. Such acceptance may be subject to 

the terms of any restrictive or affirmative covenant, or condition of servitude...” (Fish 

and Wildlife Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 2 of 7 

Description of Use: 

At the scoping meetings for the Sweetwater Marsh and South San Diego Bay Units of the 

San Diego Bay NWR Comprehensive Conservation Plan (CCP), the public expressed a 

desire to see the existing opportunities for wildlife observation and photography on 

Gunpowder Point continued. There was also an interest in developing additional wildlife 

observation opportunities in the vicinity of Paradise Marsh. Wildlife observation and 

photography represent two of the six priority public uses of the National Wildlife Refuge 

System that if determined to be compatible uses should be facilitated on National Wildlife 

Refuges. 

As described in the Public Use Program discussion in Section 2.2.2.1 of the Final CCP/ 

Environmental Impact Statement (EIS) (USFWS 2006), existing opportunities for wildlife 

observation and photography on the Sweetwater Marsh Unit are currently provided on 

Gunpowder Point. From the Chula Vista Nature Center, an observation pavilion located 

near the edge of the bay, and portions of the existing interpretive trail system (refer to Figure 

2-1 of the Final CCP/EIS), Refuge visitors can observe migratory birds foraging within the 

salt marshes and tidal mudflats located adjacent to Gunpowder Point. Also available from 

the observation pavilion and portions of the trail system, are the sights and sounds of birds, 

such as black brant (Branta bernicla nigricans) and elegant tern (Thalasseus elegans), 

foraging and loafing in the bay. Although no new opportunities for wildlife observation and 

photography are proposed on Gunpowder Point, the CCP does include a proposal to redesign 

the existing interpretive trail system (refer to the Compatibility Determination prepared for 

environmental education and interpretation on the Sweetwater Marsh Unit, as well as Section 

2.2.2.3 of the Final CCP/EIS). It is anticipated that this redesign would improve 

opportunities for wildlife observation. 

 

Public access onto Gunpowder Point is only available via a bus that transports visitors from a 

satellite parking area (located to the east of the Refuge) to the Chula Vista Nature Center. 

The City of Chula Vista, which operates this shuttle bus, does not collect a fee to use the bus; 

however, an admission fee is collected to enter the facilities operated by the Chula Vista 

Nature Center. No fee is collected from visitors interested only in observing wildlife from 

the existing trail system and observation pavilion on Gunpowder Point. Public access onto 

the Refuge is permitted during those hours in which the Chula Vista Nature Center is open 

(Tuesday through Sunday, 10:00 AM - 5:00 PM, except major holidays). Approximately 

35,000 people visited the Nature Center during 2003 and many of these visitors spend time 

on the interpretive trails located on the Refuge. 

Appropriate upland sites are not available on Refuge property in the vicinity of Paradise 

Marsh or F&G Street Marsh to accommodate new opportunities for wildlife observation. 

Therefore, to address the public’s request for wildlife observation sites in these areas, the 

CCP recommends that the Refuge Manager coordinate with adjacent local agencies (National 

City and Chula Vista) to develop wildlife observation sites within the public rights-of-way 

that abut Paradise Marsh and the F&G Street Marsh (see Figure 1-3 of the Final CCP/EIS). 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 3 of 7 

Availability of Resources: 

Direct costs to administer opportunities for wildlife observation and photography, including 

monitoring of trail user activities, are primarily in the form of staff time. Adequate staff 

positions and financial resources are currently available and committed to manage the 

continuation of existing opportunities for wildlife observation and interpretation on 

Gunpowder Point. To adhere to the stipulation regarding additional regulatory signage on 

the Refuge, approximately $5,000 would be required to fabricate and install up to five signs 

on the Refuge. There is adequate funding in the current budget to cover this expense. The 

development of observation areas in the vicinity of Paradise Marsh and F&G Street Marsh 

would require participation by the adjoining property owners, which in this case are the 

Cities of National City and Chula Vista, respectively. Funding is not currently available in 

the Refuge budget to assist in the construction of observation areas in these locations, 

however, potential future funding sources could include Federal cost share grants, other state 

or local grants, private donations, and/or contributions from the Refuge’s Friends Group. 

Anticipated Impacts of the Use: 

Activities related to wildlife observation and photography can result in negative impacts to 

wildlife by altering wildlife behavior, reproduction, distribution, and habitat (DeLong and 

Schmidt 2000). In addition, birds frequently approached by humans engaged in these 

activities may reduce foraging times in the affected area or avoid the area entirely (Huffman 

1999). During studies conducted in south San Diego Bay, Huffman observed that human 

activity along the shoreline and in the mudflats would flush all birds within a 50 to 100 meter 

radius. To minimize these types of impacts within the Sweetwater Marsh Unit, various 

measures have been implemented in an attempt to keep individuals within designated 

observation areas and out of sensitive habitats. These measures include post and cable 

fencing, regulatory signage, and periodic monitoring of trail user activities. 

Endangered and Threatened Species: Human activity can have adverse impacts to listed 

species, particularly when avian nesting or foraging activities are disrupted. Of particular 

concern are potential disturbances to the endangered light-footed clapper rail (Rallus 

longirostris levipes), which is supported by the salt marsh habitat that occurs on the Refuge. 

Maintaining designated trails to accommodate wildlife observation and photography, as well 

as regulatory and interpretive signage to keep authorized users out of sensitive areas, has 

minimized disturbance to this species. Another Federally-listed endangered species that is 

susceptible to harm as a result of off-trail activity is the salt marsh bird’s beak (Cordylanthus 

maritimus maritimus), an annual plant found in the high marsh. The measures described 

above also minimize the potential for impacts to this species as a result of authorized wildlife 

observation and photography activities on the Refuge. However, to further minimize the 

potential for disturbance to these species, as well as to reduce the amount of unauthorized 

access onto the Refuge from adjoining parcels, additional signage would be installed to keep 

the public out of sensitive habitat areas. 

 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 4 of 7 

Public uses such as wildlife observation and photography are only permitted on Gunpowder 

Point, the remainder of the Refuge is closed to public access in an effort protect sensitive 

habitat and the endangered and threatened species and migratory birds supported by that 

habitat. As a result, no impacts to the endangered California least tern (Sternula antillarum) 

or threatened western snowy plover (Charadrius alexandrinus nivosus) are anticipated. 

Sensitive Habitats: Opportunities for wildlife observation and photography are generally 

limited to the area in and around the Chula Vista Nature Center and on the existing trail 

system, therefore, impacts to sensitive habitats as a result of these uses would be minimal 

(refer to the discussion provided under Endangered and Threatened Species). 

Migratory Birds: The existing trail system provides access to the edge of the Refuge where 

expansive mudflats provide foraging habitat during low tides. To minimize off-trail activity 

in this area, post and cable fencing has been installed along the trails. Additional signage is 

recommended in areas where these trails abut sensitive habitat to further potential impacts. 

 

Public Review and Comment: 

Wildlife observation and photography have been discussed a several occasions at public 

workshops held in conjunction with the Comprehensive Conservation Plan (CCP) process. 

To initiate the CCP process, a Notice of Intent was published in the Federal Register on June 

23, 2000 (65 FR 39172). At that time, written comments were solicited. In July 2000, two 

initial scoping meetings were held, one in Imperial Beach and one in Chula Vista, to receive 

input from the public on issues related to the South San Diego Bay and Sweetwater Marsh 

Units. Due to the public’s level of interest in these refuges, focused public workshops were 

held in September 2000 and June 2001 to specifically address the issue of public use. Three 

additional workshops were held between November 2000 and May 2001 to receive input 

from the public on wildlife management and restoration proposals for these refuges. All of 

the public meetings were well attended with at least 40 people present at each meeting. 

Approximately 50 to 60 people attended those meetings related to public use. 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. One of these updates was devoted entirely to the topic of 

public use. These Planning Updates have been distributed to more than 1,000 individuals 

and organizations representing interested members of the public, conservation organizations, 

hunting, fishing and boating organizations, public agencies, municipalities, special districts, 

Tribes, and adjoining property owners. We received more than 50 letters, emails, and phone 

calls related to public use between June and November 2001 and numerous other 

communications relevant to public uses on the Refuge were received in 2002 and 2003. 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 5 of 7 

During the scoping meetings and public use workshops for the CCP, a number of individuals 

expressed a general desire to see additional opportunities for wildlife observation and 

photography within the south bay, however, most of the site specific suggestions related to 

the South San Diego Bay Unit. The one recommendation that related to the Sweetwater 

Marsh Unit involved a request to see opportunities for wildlife observation and interpretation 

in the vicinity of Paradise Marsh in the northern end of the Refuge. 

The draft Compatibility Determination for wildlife observation and photography on the 

Sweetwater Marsh Unit was circulated for public review and comment as part of the San 

Diego Bay National Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental 

Impact Statement (CCP/EIS). Specifically, it was included in Appendix K of the draft 

CCP/EIS. The Notice of Availability for the draft CCP/EIS was published in the Federal 

Register on July 22, 2005 and a Planning Update announcing the availability of the draft was 

sent to over 1,000 individuals, agencies, non-governmental organizations, and other 

stakeholders. In addition, the draft CCP/EIS was provided to over 275 interested parties and 

made available for review on the Refuge’s CCP website. Public comments were accepted 

through September 19, 2005. No comments related to this Compatibility Determination were 

received during the public comment period. 

Determination: 

 Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations Necessary to Ensure Compatibility: 

The following measures will be taken to minimize impacts to wildlife: 

1. To discourage off-trail activity “Closed Area” or “Sensitive Habitat” signs will be 

installed in areas where trails or observation areas abut sensitive habitat. 

2. Periodic monitoring of trail user activities will continue to determine if unauthorized 

off-trail activity is occurring in or around sensitive areas of the Refuge. If during 

monitoring it is determined that off-trail activity could result in impacts to Refuge 

resources, the Refuge Manager shall implement measures, such as additional signage, 

fencing, and/or barrier plantings, to further discourage this activity. 

 

Justification:

The continuation of wildlife observation and photography on Gunpowder Point and the 

possible expansion of wildlife observation opportunities in the vicinity of Paradise Marsh 

and F&G Street Marsh would not adversely affect the Refuge’s wildlife or its habitat. In 

addition, as the public engages in these types of activities on the Refuge, many will go away 

with a greater understanding of the importance of protecting native habitats and their 

associated wildlife species. The overall benefits of facilitating these uses would support the 

purposes of the Refuge by improving opportunities for managing, conserving, and protecting 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 6 of 7 

fish and wildlife resources. In the same manner, allowing the public to observe the wildlife 

that is being protected within the Refuge without materially interfering with their daily 

activities supports the fulfillment the National Wildlife Refuge System (System) mission’s of 

wildlife first. The National Wildlife Refuge System Improvement Act (the Act) states that 

“compatible wildlife-dependent recreation is a legitimate and appropriate general public use 

of the System, directly related to the mission of the System...and through which the 

American public can develop an appreciation for fish and wildlife...” Wildlife observation 

and photography are two of the six priority public uses of the System, as defined by the Act, 

that when found to be compatible, should be facilitated. The continuation of these programs 

would implement the Refuge goal of fostering a broader understanding of the value of, and 

need for, wildlife conservation.

Mandatory Re-Evaluation Date: 

 X Mandatory 15-year Re-Evaluation Date (for priority public uses) 

 Mandatory 10-year Re-Evaluation Date (for all uses other than priority public uses) 

NEPA Compliance for Refuge Use Decision: 

__Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited:

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance 

on Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater 

National Wildlife Refuge (Draft). 

Huffman, Kathy. 1999. San Diego South Bay Survey Report – Effects of Human Activity 

and Water Craft on Wintering Birds in the South San Diego Bay. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 
Final Wildlife Observation and Photography CD – Sweetwater Marsh Unit 

Page 7 of 7 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 1 of 11 

Compatibility Determination

- FINAL - 

Use: Environmental Education and Interpretation 

Refuge Name: Sweetwater Marsh Unit of the San Diego Bay National Wildlife Refuge 

 (San Diego County, Cities of Chula Vista and National City, California) 

 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the Sweetwater Marsh Unit are the Endangered 

Species Act of 1973, as amended (16 U.S.C. §§1531-1543); Fish and Wildlife Act of 1956, 

as amended (16 U.S.C. §§742a-742j, not including 742d-742l); and the Fish and Wildlife 

Coordination Act of 1934, as amended (16 U.S.C. §§661-667e). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge (NWR) was established: 

“to protect, manage, and restore habitats for federally listed endangered and 

threatened species and migratory birds, and to maintain and enhance the biological 

diversity of native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species 

Act of 1973, as amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as 

amended); 

”...for the development, advancement, management, conservation, and protection of 

fish and wildlife resources...for the benefit of the United States Fish and Wildlife 

Service, in performing its activities and services. Such acceptance may be subject to 

the terms of any restrictive or affirmative covenant, or condition of servitude...” (Fish 

and Wildlife Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 2 of 11 

Description of Use: 

Environmental Education: As described in the Public Use Program discussion in Section 

2.2.2.1 of the Final San Diego Bay NWR Comprehensive Conservation Plan 

(CCP)/Environmental Impact Statement (EIS) (USFWS 2006), the Sweetwater Marsh Unit is 

currently the setting for several environmental education programs involving students from 

Chula Vista and National City, as well as from the greater San Diego region. These 

programs represent a collaborative effort between the Service, the Chula Vista Nature 

Center, National City, several school districts, and nonprofit organizations. One program, 

implemented by the Chula Vista Elementary School District, focuses on a science and social 

studies curriculum. The program serves some 12,000 kindergarten through 12th grade 

students annually. The Refuge, specifically Gunpowder Point (refer to Figure 2-1 of the 

Final CCP/EIS), provides the outdoor classroom for this program where students study topics 

such as the tides, water quality, native vegetation, and birds. 

Another program, created by the San Diego Zoological Society, Chula Vista Nature Center, 

and the San Diego NWR Complex through a grant to the Zoo’s Habitat Conservation 

Education Department, is Sweetwater Safari. This program, which meets the State of 

California’s science standards for fourth grade, was created for students to learn about 

science and the local environment through a hands-on experience. The program includes onsite curriculum that is conducted on the refuge and a post-visit curriculum that is conducted 

in the classroom. The on-site curriculum is taught by the teachers. To lead the self-guided 

on-site program, which takes place on Gunpowder Point, the teacher must first participate in 

a training session conducted by Refuge staff, Chula Vista Nature Center staff, and other 

volunteer teachers. These training sessions, which are provided free of charge, are conducted 

quarterly at the Chula Vista Nature Center. Once a teacher has completed this training, he or 

she can arrange a time with the Nature Center to guide his/her class through the program. 

Equipped with backpacks containing relevant educational materials, the class travels along 

the 0.5 mile trail system on Gunpowder Point gathering information regarding the many 

resources supported by the Refuge. The Refuge trails are flat, wide and wheelchair 

accessible. Transportation grants to bring student onto the refuge are available for this 

program. 

Another program supported by the Refuge is conducted by Kimball Elementary School in 

National City. This program, which generally occurs just upstream of the Refuge, presents a 

science and mathematics-based curriculum focused on the protection of watersheds, the 

function of wetland systems, and water quality testing. 

The Refuge also partners with the Chula Vista Nature Center, San Diego Zoo, Kimball 

Elementary, Paradise Creek Educational Park, Aquatic Adventures, and others to facilitate 

occasional field trips to the Refuge to support the organizations’ desire to introduce students 

to the biological and cultural resources of the region, including those resources supported on 

the refuge. The majority of these programs incorporate language arts, math, and social 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 3 of 11 

sciences into their curriculum in accordance with California State Education Standards. 

Several of these programs have been developed to reach the underserved youth of the region 

whose opportunities to experience the natural environmental first hand may be limited. 

Environmental education programs are conducted on the Refuge once or twice a week 

throughout the year, with field trip opportunities open to only one classroom of 

approximately 32 students per day. Participants are generally transported to the site by bus 

or van. In some cases, the students use the existing shuttle bus that provides access to the 

Refuge from a satellite parking facility located off Refuge property. 

The environmental education community has also expressed a desire to have the various 

environmental programs available within the south bay coordinated by a single point of 

contact, a South Bay environmental education facilitator. The Refuge Complex proposes to 

partner with other agencies and institutions in the region to support the creation of and 

identify funding for such a position. This environmental education facilitator would be 

responsible for contacting school districts about the many field experience curricula available 

in the South Bay, including those on the Sweetwater Marsh Unit, developing a region-wide 

strategy for filling teacher workshops, soliciting transportation grants to be used by each 

program, and developing teacher in-service agreements with local school districts to more 

efficiently reach the greatest number of educators. 

Environmental Interpretation: Interpretation of the many resources found on the Sweetwater 

Marsh Unit is currently provided through a series of interpretive panels installed along an 

existing half-mile trail system located on Gunpowder Point (refer to Figure 2-4 of the Final 

CCP/EIS). These panels provide general information about the coastal resources protected 

within the Refuge. Additional interpretation of the historic resources on Gunpowder Point is 

also provided along the trail system. Several of the existing interpretive elements along these 

trails are in need of refurbishment and/or replacement. 

Public access onto the Refuge is only available via a bus that transports visitors from a 

satellite parking area (located east of the Refuge) to the Chula Vista Nature Center. The City 

of Chula Vista, which operates this shuttle bus, does not collect a fee to use the bus; 

however, an admission fee is collected at the Nature Center, should visitors wish to enter the 

facilities operated by the Chula Vista Nature Center. No fee is collected from visitors 

interested only in walking along the existing trail system. Public access onto the Refuge is 

permitted during those hours in which the Chula Vista Nature Center is open (Tuesday 

through Sunday, 10:00 AM - 5:00 PM, except major holidays). Approximately 35,000 

people visited the Nature Center during 2003 and many of these visitors spend time on the 

interpretive trails located on the Refuge. 

 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

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The Chula Vista Nature Center, which is located on Refuge lands that are leased to the City 

of Chula Vista, includes exhibits and signs that interpret Refuge resources, as well as the 

many biological resources of San Diego Bay. Included within the Nature Center are several 

live animal exhibits, including an aviary that includes various shorebirds commonly found in 

the area and a breeding pair of light-footed clapper rails. Several times a week, Nature 

Center docents lead small groups of people on interpretive walks along the Refuge’s trail 

system. 

The public has expressed a desire to not only see uses related to environmental interpretation 

continued on the Refuge, but also to see the existing opportunities expanded to reach a larger 

segment of the surrounding community. To improve opportunities for environmental 

interpretation, a step-down interpretive trail plan is proposed for Gunpowder Point. This 

plan would address the need to replace outdated interpretive panels and would include 

designs for new interpretive elements. The plan would also include an evaluation of the 

existing trail system on Gunpowder Point and where necessary propose a realignment of 

current trails to provide better coordination with the educational and interpretive programs 

occurring on the Refuge. This trail system, to be referred to as The Discovery Trail, would 

be provided primarily for the purpose of facilitating the Refuge’s environmental education 

and interpretation programs. The redesigned trail system would also improve opportunities 

for wildlife observation and photography. 

 

To address the public’s desire to expand opportunities for environmental interpretation in 

other portions of the Refuge, the Refuge Manager would coordinate with adjacent local 

agencies (National City and Chula Vista) to develop interpretive elements within the public 

rights-of-way that abut Paradise Marsh and the F&G Street Marsh (refer to Figure 2-4 of the 

Final CCP/EIS). 

 

Availability of Resources: 

Direct costs to administer the current environmental education and interpretation programs 

are in the form of staff time. One environmental education program that includes all fourth 

grade students in the City of Chula Vista is administered and funded by the City of Chula 

Vista. The development and implementation of another program, Sweetwater Safari, was 

initially funded by a grant, while the responsibility for training is shared by Refuge staff and 

the Nature Center. 

Additional funding would be required to prepare and implement a step-down interpretive 

trail plan for Gunpowder Point to expand and improve interpretive opportunities on the 

Refuge. Major construction expenses would involve replacing existing interpretative signage 

and creating new trail segments, while also closing and restoring other segments. The 

estimated cost to the Complex for current refuge education programs is under $500 per year. 

 This includes material costs and some staff time for occasional oversight of the programs, 

periodic updates to the current curriculum, and participation in teacher training sessions. 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

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To implement and administer the proposed environmental education and interpretive 

programs described, the following staffing and materials/facilities would be required: 

Staffing 

Position Involvement FTE Cost 

Project Leader/Deputy 

Project Leader 

General oversight of programs 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.4 $36,400 

Refuge Operations 

Specialist 

Periodic on-site oversight, occasional 

monitoring of program activities 0.3 $26,000 

Wildlife Biologist Monitoring, reporting, assistance in 

program development, oversight of 

biological technician 

0.3 $26,000 

Information and 

Education Specialist 

Coordinate and provide oversight of 

environmental education programs and 

assist in interpretive plan design 0.3 $23,400 

Outdoor Recreation 

Planner 

Evaluate and redesign as required the 

existing interpretive trail system, assist in 

the design and siting of new interpretive 

signage, supervise trail construction 

0.5 $22,750 

Law Enforcement Officer Law enforcement 0.3 $20,800 

Park Ranger Assist in trail realignment and installation 

of interpretive signage, facilities 

maintenance 

0.3 $13,000 

Biological Technician Field data collection, assistance with 

monitoring, analysis, and report writing 0.3 $15,170 

TOTAL FTES AND 

COSTS FOR STAFFING 3.1 $231,220 

Facilities 

Material/Facility 

Required 

Explanation of Need Cost 

Education materials and 

supplies 

Various materials are required annually to implement 

existing environmental education programs $500 

Prepare a step-down 

interpretive trail plan for 

Gunpowder Point 

Design new interpretive signs and redesign the 

existing trail system to better facilitate the Refuge’s 

environmental education and interpretation programs 

$35,000 

Refurbished and/or new 

interpretive elements 

Updated existing interpretative signs to better 

facilitate education and interpretation programs. $50,000 

Realign/refurbish 

existing trail system 

New trail construction would be required to 

implement the step-down interpretative trail plan $25,000 

Interpretive elements to 

be installed along public 

right-of-ways 

Contribute funds to assist in the installation of 

interpretive elements along designated public rightsof-way near Paradise Marsh and F&G Street Marsh. 

$10,000 

TOTAL COST FOR 

FACILITIES $120,200 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 6 of 11 

Adequate staff positions and financial resources are currently available and committed to 

manage the continuation of existing opportunities for environmental education and 

interpretation. However, the current Refuge budget is not adequate to fund the development 

and implementation of a step-down interpretive trail plan. The plan itself would be 

developed to address the current status of the existing trail system and the identification of 

appropriate realignments of some trails and the closure and revegetation of others. Also 

included in the plan would be designs for updated interpretive elements that would better 

coordinate with the environmental education programs conducted on the Refuge. In light of 

budget shortfall, project could be broken into phases funding sources are identified. 

Potential sources for additional funding include Federal cost share grants, state grants that 

focus on environmental education, private funding sources, and contribution from the 

Refuge’s Friends group. 

Anticipated Impacts of the Use: 

Potential impacts associated with the continued and expanded implementation of 

environmental education and interpretation programs would be similar to those described in 

the Compatibility Determination prepared for wildlife observation and interpretation on the 

Sweetwater Marsh Unit. Such impacts can include disturbance to wildlife and trampling or 

damage to native habitats and sensitive plant species. These types of impacts would be 

minimized through appropriate program design, adequate Refuge oversight and supervision 

of educational activities, and ongoing coordination among partners. 

 

Endangered and Threatened Species: Human activity can have adverse impacts to 

endangered and threatened species, particularly when avian nesting or foraging activities are 

disrupted. Of particular concern are potential disturbances to the Federally-listed endangered 

light-footed clapper rail (Rallus longirostris levipes), which is supported by the salt marsh 

habitat that occurs on the Refuge. Maintaining designated trails to accommodate 

environmental education and interpretation activities has minimized disturbance to this 

species. Another Federally-listed endangered species that is susceptible to harm as a result 

of off-trail activity is the salt marsh bird’s beak (Cordylanthus maritimus maritimus), an 

annual plant found in the high marsh. Through appropriate supervision of students and the 

use of post and cable fencing along the trail, the potential for impacts has been minimized. 

 

Activities related to environmental education and interpretation occur almost exclusively on 

Gunpowder Point, as a result, no adverse impacts to the endangered California least tern 

(Sternula antillarum) or threatened western snowy plover (Charadrius alexandrinus nivosus) 

are anticipated due to the continuation of these uses on the Refuge. 

Interpretive elements proposed adjacent to Paradise Creek and F&G Street Marsh would 

occur within existing public access rights-of-way outside the boundaries of the marsh, 

therefore, the potential for impacts to the light-footed clapper rail and salt marsh bird’s beak 

would be minimal. 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

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Sensitive Habitats: The environmental education programs conducted on the Refuge utilize 

an existing trail system on Gunpowder Point to explore the resources present on the Refuge 

This trail system is clearly delineated with post and cable fencing and students are supervised 

at all times. As a result, the potential for intentional and unintentional intrusion into sensitive 

habitat from this use is minimal. 

Interpretive programs conducted on Gunpowder Point could be self-guided or lead by Chula 

Vista Nature Center docents. These activities would be confined to a designated system of 

trails on Gunpowder Point, therefore, the potential for off trail activity is low. Despite these 

measures, there would still be the potential for self-guided visitors to leave the trail and enter 

sensitive areas. The highest potential for such activities is at the end points of the existing 

trail system, where the trail brings users to the edge of sensitive habitat and then stops. In 

these areas, users may be temped to travel beyond the existing post and cable fencing to gain 

better views of the adjacent mudflats or salt marsh habitats. As described in the 

Compatibility Determination for wildlife observation and photography for the Sweetwater 

Marsh Unit, realigning the trail to provide a loop system, thereby avoiding dead-end trails, 

would minimize the potential for such off-trail activity. 

New interpretive elements proposed adjacent to Paradise Marsh and F&G Street Marsh 

would be placed within existing public access rights-of-way where no impacts to sensitive 

resources are anticipated. 

Migratory Birds: The existing trail system provides access to the edge of the Refuge where 

expansive mudflats provide foraging habitat during low tides. Off-trail human activity in this 

area could result in disturbances to foraging migratory birds. Various studies have shown 

that frequent human disturbance can negatively impact wildlife by altering wildlife behavior, 

reproduction, distribution, and habitat (DeLong and Schmidt 2000). In addition, birds 

frequently approached by humans engaged in these activities may reduce foraging times in 

the affected area or avoid the area entirely (Huffman 1999). During studies conducted in 

south San Diego Bay, Huffman observed that human activity along the shoreline and in the 

mudflats would flush all birds within a 50 to 100 meter radius. To minimize these types of 

impacts within the Sweetwater Marsh Unit, various measures have been implemented in an 

attempt to keep individuals on the designated trail and out of sensitive habitats. These 

measures include post and cable fencing along the trail, regulatory signage at trail ends, and 

periodic monitoring of trail user activities. 

Public Review and Comment: 

Environmental education and interpretation have been discussed on several occasions at 

public workshops held in conjunction with the Comprehensive Conservation Plan (CCP) 

process. To initiate the CCP process, a Notice of Intent was published in the Federal 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 8 of 11 

Register on June 23, 2000 (65 FR 39172). At that time, written comments were solicited. In 

July 2000, two initial scoping meetings were held, one in Imperial Beach and one in Chula 

Vista, to receive input from the public on issues related to the South San Diego Bay and 

Sweetwater Marsh Units. Due to the public’s level of interest in these refuges, focused 

public workshops were held in September 2000 and June 2001 to specifically address the 

issue of public use. Three additional workshops were held between November 2000 and 

May 2001 to receive input from the public on wildlife management and restoration proposals 

for these refuges. All of the public meetings were well attended with at least 40 people 

present at each meeting. Approximately 50 to 60 people attended those meetings related to 

public use. 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. One of these updates was devoted entirely to the topic of 

public use. These Planning Updates have been distributed to more than 1,000 individuals 

and organizations representing interested members of the public, conservation organizations, 

hunting, fishing and boating organizations, public agencies, municipalities, special districts, 

Tribes, and adjoining property owners. We received more than 50 letters, emails, and phone 

calls related to public use between June and November 2001 and numerous other 

communications relevant to public uses on the Refuge were received in 2002 and 2003. 

At the scoping meetings and public workshops for the CCP, the public expressed a desire to 

see the existing opportunities for environmental education and interpretation on the 

Sweetwater Marsh Unit continued. There were several recommendations to expand the 

current educational program. One individual suggested that opportunities for high school 

students be expanded. Another person recommended that additional interpretive 

opportunities be provided in the vicinity of Paradise Marsh and the F&G Street Marsh. 

Several community members commented that the Refuge’s education and interpretive 

programs could reach a broader audience if the programs included multi-lingual outreach 

materials. 

The draft Compatibility Determination for environmental education and interpretation on the 

Sweetwater Marsh Unit was circulated for public review and comment as part of the San 

Diego Bay National Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental 

Impact Statement (CCP/EIS). Specifically, it was included in Appendix K of the draft 

CCP/EIS. The Notice of Availability for the draft CCP/EIS was published in the Federal 

Register on July 22, 2005 and a Planning Update announcing the availability of the draft was 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 9 of 11 

sent to over 1,000 individuals, agencies, non-governmental organizations, and other 

stakeholders. In addition, the draft CCP/EIS was provided to over 275 interested parties and 

made available for review on the Refuge’s CCP website. Public comments were accepted 

through September 19, 2005. No comments related to this Compatibility Determination were 

received during the public comment period. 

Determination: 

 Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations Necessary to Ensure Compatibility: 

The following measures will be taken to ensure compatibility for environmental education 

and interpretation: 

Prior to implementing a new environmental education program within this Refuge Unit, the 

various parties developing the program shall coordinate with the Refuge Manager to agree 

upon appropriate times of the year to conduct the program, access routes, maximum number 

of participants per visit, and appropriate activities to be conducted. All individuals who will 

be conducting these programs shall be made aware of these conditions. 

The Refuge’s Information and Education Specialist will review all materials and programs to 

ensure consistency with Refuge goals and the mission of the National Wildlife Refuge 

System. 

“Closed Area” signs will be installed at the end of all trails leading to the edge of the bay. 

Prior to installing any new interpretive elements at Paradise Marsh and F&G Street Marsh, 

the Refuge Manager shall review the sites to verify that no impacts to Refuge resources 

would occur as a result of anticipated human activity around the interpretive elements. 

Justification:

The continuation and expansion of environmental education and interpretation uses on the 

Sweetwater Marsh Unit would not adversely affect the Refuge’s wildlife or its habitat. In 

addition, as the public engages in these types of activities on the Refuge, many will go away 

with a greater understanding of the importance of protecting native habitats and their 

associated wildlife species. The overall benefits of facilitating these uses would support the 

purposes of the Refuge by improving opportunities for managing, conserving, and protecting 

fish and wildlife resources. In the same manner, presenting the public with information 

about the importance of the resources supported on the Refuge without materially interfering 

with their daily activities supports the fulfillment the National Wildlife Refuge System 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 10 of 11 

(System) mission’s conservation mission. The National Wildlife Refuge System 

Improvement Act (the Act) states that “compatible wildlife-dependent recreation is a 

legitimate and appropriate general public use of the System, directly related to the mission of 

the System...and through which the American public can develop an appreciation for fish and 

wildlife...” Environmental education and interpretation are two of the six priority public uses 

of the System, as defined by the Act, that when found to be compatible, should be facilitated. 

 The continuation of these programs would implement the Refuge goal of fostering a broader 

understanding of the value of, and need for, wildlife conservation. 

 

Mandatory Re-Evaluation Date: 

 X Mandatory 15-year Re-Evaluation Date (for priority public uses) 

 Mandatory 10-year Re-Evaluation Date (for all uses other than priority public uses) 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited: 

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance 

on Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater 

National Wildlife Refuge (Draft). 

Huffman, Kathy. 1999. San Diego South Bay Survey Report – Effects of Human Activity 

and Water Craft on Wintering Birds in the South San Diego Bay. 

U.S. Fish and Wildlife Service. 1985. Salt Marsh Bird’s Beak (Cordylanthus maritimus subsp. 

maritimus) Recovery Plan. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 
 

Final Environmental Education/Interpretation CD – Sweetwater Marsh Unit 

Page 11 of 11 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 1 of 9 

Compatibility Determination

-FINALUse: Mosquito Management

Refuge Name: Sweetwater Marsh Unit of the San Diego Bay National Wildlife Refuge 

 (San Diego County, Cities of Chula Vista and National City, California) 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the Sweetwater Marsh Unit are the Endangered 

Species Act of 1973, as amended (16 U.S.C. §§1531-1543); Fish and Wildlife Act of 1956, 

as amended (16 U.S.C. §§742a-742j, not including 742d-742l); and the Fish and Wildlife 

Coordination Act of 1934, as amended (16 U.S.C. §§661-667e). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge (NWR) was established: 

“to protect, manage, and restore habitats for federally listed endangered and 

threatened species and migratory birds, and to maintain and enhance the biological 

diversity of native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species 

Act of 1973, as amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as 

amended); 

”...for the development, advancement, management, conservation, and protection of 

fish and wildlife resources...for the benefit of the United States Fish and Wildlife 

Service, in performing its activities and services. Such acceptance may be subject to 

the terms of any restrictive or affirmative covenant, or condition of servitude...” (Fish 

and Wildlife Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 2 of 9 

Description of Use:

Mosquito management throughout the coastal refuges of San Diego County is conducted 

under the auspices of a Refuge Special Use Permit (SUP) in coordination with the San Diego 

County Department of Environmental Health, Vector Control Division. The SUP is issued 

annually. The primary purpose for implementing mosquito management on this Refuge is to 

avoid threats to public or wildlife health from specific mosquito-borne disease. Mosquito 

management is implemented on the Sweetwater Marsh Unit through a phased approach that 

emphasizes early detection and treatment, if warranted, with larvicides. The use of 

adulticides is to be reserved for addressing human health emergencies. 

 

Several mosquito species are expected to occur in the vicinity of the Refuge that are capable 

of transmitting microbial organisms that cause human diseases such as malaria and 

encephalitis. The mosquitoes of major concern in California belong to the genera Culex, 

Ochlerotatus, and Anopheles. The species of greatest public health concern include Culex 

tarsalis, Culex pipiens, Culex quinquefasciatus and Anopheles hermsi. Of lesser importance 

are the salt marsh mosquitoes: Ochlerotatus squamiger and Ochlerotatus taeniorhynchus. 

The closest mosquito traps to the Sweetwater Marsh Unit are located at the Otay River and 

Hollister Street. These traps are monitored by the County of San Diego, Department of 

Environmental Health, Vector Control Division. The data collected from these traps in 2003 

indicates that eight species of mosquito are commonly found in the general area, however, to 

date, the degree to which each of these species occurs within the Sweetwater Marsh Unit has 

not determined. The most common species found in the Otay traps include: 

Anopheles hermsi – This species, which is very commonly found in the Otay traps, is a 

highly competent vector of malaria, although this disease is not prevalent in this region. 

Culex erythrothorax – This species, which is the most common mosquito in San Diego, is 

typically considered a nuisance. It is commonly found in the Otay traps and occurs in 

densely vegetated freshwater marshes and heavily vegetated backwater zones. It is not 

considered to be a major disease carrier, although its ability to potentially harbor West Nile 

Virus (WNV) is currently unknown. 

Culex tarsalis – A highly competent vector mosquito, this species is quite common in the 

Otay traps. Viewed generally as a nuisance mosquito, this species can also be an effective 

carrier of disease. 

Culiseta incidens and Culiseta particeps – These two species are regularly captured in the 

Otay traps in small to moderate numbers. Neither species is considered to be a disease 

vector, but can be a biting nuisance. Their ability to harbor WNV is unknown. 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

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Ochlerotatus increpitus – Primarily a nuisance mosquito, this species, which bites during the 

day, is common in the Otay traps. Its ability to vector WNV is unknown. 

Ochlerotatus taeniorhynchus and Ochlerotatus squamiger – These mosquito species are 

prevalent in salt marsh habitat. Ochlerotatus taeniorhynchus is primarily a day-biting 

nuisance, and neither species is currently considered to be a disease carrier; however their 

ability to transmit WNV is unknown. 

Mosquito management on the Sweetwater Marsh Unit is addressed through an integrated pest 

management approach in which Refuge and County vector control officials coordinate efforts 

to manage the overall environmental health of adjacent communities while minimizing 

impacts to Refuge trust resources. County and Refuge staff work together to agree upon 

issues related to access, methods of operation, and timing of access, as well as to exchange 

information related to listed species occurrences, permitting, and relevant agency policy. 

The current procedures for implementing mosquito management on this Refuge involve an 

annual meeting between County and Refuge staff to coordinate all necessary permitting and 

implementation planning required to conduct mosquito monitoring and control on the Refuge 

for the upcoming year. Issues such as access points and pathways to be used by County 

personnel, appropriate hours of operation, and requirements for field coordination are 

discussed, agreed upon, and incorporated into the SUP. As part of this coordination process, 

County vector control personnel are provided with data generated by the Refuge biologist on 

listed species and other trust resources. County personnel share relevant data related to 

mosquito and disease monitoring in the vicinity of the Refuge. In addition, periodic 

meetings are conducted in the field with County field staff and the Refuge biologist to further 

coordinate activities. These meetings are scheduled throughout the season when warranted 

to ensure protection of endangered and threatened migratory birds and to avoid disturbance 

to nesting birds. 

Following the conditions included in the SUP, County vector control personnel conduct 

periodic mosquito larvae surveys in many discrete areas throughout the Refuge. Because the 

primary means of mosquito management is the use of larvicides, it is essential that larvae be 

observed prior to pupation so that they may be treated appropriately by the least 

environmentally damaging means. As a result, the frequency of larvae surveys increases 

throughout the mosquito breeding season. Currently, treatment areas are determined based 

on the season, the species and density of the mosquitoes detected, the proximity of the 

vectors to surrounding urban areas, and the life stage the mosquitoes are found in. Control of 

adult or pupal mosquitoes is not currently conducted on the Refuge. 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 4 of 9 

Public concern over human health issues related to mosquito-borne disease has intensified on 

the west coast with the advance of WNV across the United States. To address mosquito 

management, a phased response strategy has been developed for implementation on refuges 

in the Pacific Region. This strategy encourages an integrated pest management approach that 

incorporates habitat and best management practices to reduce the need for and use of 

insecticides on refuges, while also ensuring that legitimate human, fish, and wildlife health 

concerns are addressed. To implement this phased response strategy, the current procedures 

for managing mosquitoes on this Refuge will be augmented to better identify thresholds for 

mosquito treatment and presents specific responses to various conditions encountered in the 

field. Under this new program, if mosquito population monitoring and disease surveillance 

(implemented by County vector control personnel) indicate that human health thresholds are 

exceeded, the use of larvicides, pupicides, and/or adulticides may become necessary. In 

some cases, emergency actions may be required that are not addressed by this Compatibility 

Determination. 

 

Two larvicide compounds that could be used to manage mosquitoes on the Refuge include: 

Bti (Bacillus thuringienensis israelensis) and Altosid (methoprene). Both are larvicides 

intended to control mosquitoes in wetlands prior to their emergence as adults. Bti is used 

primarily to control early stage larvae and is available in liquid and granular formulations. 

Altosid is used on later stage mosquito larvae and is available in liquid, briquet and pellet 

formulations. Both compounds are highly specific to mosquito larvae. The use of Golden 

Bear 1111, which is effective at preventing adult mosquito emergence from wetlands but 

toxic to fish and other aquatic organisms, is not permitted within the Sweetwater Marsh Unit. 

 

Availability of Resources: 

To implement and administer mosquito management on the Sweetwater Marsh Unit, the 

following staffing and facilities are required: 

Staffing 

Position Involvement FTE Cost 

Project Leader/Deputy 

Project Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.3 $30,300 

Refuge Operations 

Specialist 

On-site oversight when 

necessary 0.3 $26,000 

Wildlife Biologist Monitoring, reporting, 

plan development, and 

oversight of vector control 

activities 

0.3 $26,000 

TOTAL FTES AND 

COSTS FOR STAFFING 1.3 $130,000 

TOTAL COST FOR 

FACILITIES 

none $0 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 5 of 9 

Adequate staff positions and financial resources are currently available and committed to 

implement mosquito management on the Sweetwater Marsh Unit. 

Anticipated Impacts of the Use: 

The purpose of this section is to critically and objectively evaluate the potential direct, 

indirect and cumulative effects mosquito management could have on the Refuge’s 

endangered and threatened species and other fish and wildlife resources. 

Habitat and Wildlife Disturbance: Vegetation trampling resulting from mosquito monitoring 

and mosquito control, as well as the possible creation of channels to drain stagnant water 

areas, could adversely impact native vegetation and wildlife habitat. In addition, these 

activities could result in disturbances to the existing wildlife that utilizes this area. At 

present, the marsh complex within the Refuge supports a variety of coastal wetland habitats 

including subtidal, intertidal mudflat, and salt marsh habitats. These wetland areas provide 

foraging, resting, and nesting habitat for a variety of birds, including migratory shorebirds, 

waterfowl, and songbirds. To minimize impacts related to disturbance, the Refuge biologist 

would coordinate with County vector control personnel at least annually to review 

appropriate conduct within these sensitive habitat areas. Specific field implementation 

protocols for working in sensitive habitat areas would be included in the Refuge SUP. No 

impacts to upland habitat are anticipated as a result of mosquito management activities. 

Endangered and Threatened Species: One of the purposes for the establishment of the 

Sweetwater Marsh NWR is to protect Federally- listed endangered or threatened species. 

Human activity can have adverse impacts on endangered and threatened species, particularly 

when this activity disrupts bird nesting or foraging. The California least tern (Sternula

antillarum) and California brown pelican (Pelecanus occidentalis californicus), both 

Federally-listed endangered species, forage within the main tidal channel within the 

Sweetwater Marsh, while the threatened western snowy plover (Charadrius alexandrinus 

nivosis) forages year round along the channel banks. The D Street Fill portion of the Refuge 

also supports least tern and western snowy plover nesting. Human activity within the 

Refuge’s main marsh complex could disrupt the foraging activity of all of these species. 

 

The Federal endangered light-footed clapper rail also occurs within Sweetwater Marsh Unit 

in the Refuge’s salt marsh and brackish marsh habitats. Threats to the light-footed clapper 

rail consist primarily of direct habitat or nest losses through trampling of cordgrass or 

pickleweed. The State endangered Belding’s savannah sparrow (Passerculus sandwichensis 

beldingi) occupies the high salt marsh vegetation throughout Sweetwater Marsh. Human 

intrusion into these areas could disrupt foraging activities, as well as result in direct habitat 

or nest losses through trampling of pickleweed. Impacts to these salt marsh species would be 

minimized through adherence to the field implementation protocols established for mosquito 

management in the Refuge SUP. 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 6 of 9 

In addition to endangered and threatened bird species, the Sweetwater Marsh Unit also 

supports the Federally-listed endangered annual plant species, salt marsh bird’s beak 

(Cordylanthus maritimus maritimus). Salt marsh bird’s beak is distributed in various 

locations throughout the marsh, primarily in upper marsh elevations that are inundated by 

tides on a regular basis, but above areas that receive daily salt water flooding. Such areas are 

more likely to be impacted by human activity in the marsh, because they are drier than other 

portions of the marsh. Yearly population numbers depend directly on seed dispersal and 

successful plant establishment. Field observations indicate that even a moderate amount of 

foot traffic can damage the fragile seedlings (USFWS 1985), resulting in decreased 

population numbers. To reduce the potential for impacts to this species, periodic meetings 

would be conducted in the field with County field staff and the Refuge biologist to identify 

sensitive areas that should be avoided during monitoring and control activities and designate 

other areas that can be accessed without concern for habitat damage. 

 

Nesting Season Disturbance: The nesting season varies with species but can generally be 

described as occurring between mid-February and mid-September. Disturbance to nesting 

bird species may occur if vector control personnel are present in the vicinity of avian nesting 

colonies or individual nests. 

Several species, four of which are state and/or Federally-listed as endangered or threatened, 

nest within the Sweetwater Marsh Unit. As described above, the habitats present within the 

marsh complex support light-footed clapper rail and Belding’s savannah sparrow nesting. 

Cordgrass stands within the marsh support clapper rail nesting, while high salt marsh 

vegetation supports savannah sparrow nesting. In addition, the California least tern and 

western snowy plover nest on the D Street Fill portion of the Refuge. To avoid impacts to 

nesting species, periodic meetings would be conducted in the field with County field staff 

and the Refuge biologist to coordinate activities and delineate sensitive nesting areas that 

should be avoided. 

Public Review and Comment:

Two public scoping meetings and a series of public workshops to discuss habitat 

management, restoration, and public use were held in conjunction with the CCP process. To 

initiate the CCP process, a Notice of Intent was published in the Federal Register on June 23, 

2000 (65 FR 39172). At that time, written comments were solicited. In July 2000, two 

initial scoping meetings were held, one in Imperial Beach and one in Chula Vista, to receive 

input from the public on issues related to the Sweetwater Marsh and South San Diego Bay 

Units. Due to the public’s level of interest in these refuges, focused public workshops were 

held in September 2000 and June 2001 to specifically address the issue of public use. Three 

additional workshops were held between November 2000 and May 2001 to receive input 

from the public on wildlife management and restoration proposals for these refuges. All of 

the public meetings were well attended with at least 40 people present at each meeting. 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 7 of 9 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. These Planning Updates have been distributed to more than 

1,000 individuals and organizations representing interested members of the public, 

conservation organizations, hunting, fishing and boating organizations, public agencies, 

municipalities, special districts, Tribes, and adjoining property owners. We received more 

than 50 letters, emails, and phone calls related to the CCP between June and November 2001 

and numerous other communications relevant to public uses on the Refuge were received in 

2002 and 2003. No public comments related to mosquito management have been received to 

date. 

The draft Compatibility Determination for mosquito management on the Sweetwater Marsh 

Unit was circulated for public review and comment as part of the San Diego Bay National 

Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental Impact Statement 

(CCP/EIS). Specifically, it was included in Appendix K of the draft CCP/EIS. The Notice 

of Availability for the draft CCP/EIS was published in the Federal Register on July 22, 2005 

and a Planning Update announcing the availability of the draft was sent to over 1,000 

individuals, agencies, non-governmental organizations, and other stakeholders. In addition, 

the draft CCP/EIS was provided to over 275 interested parties and made available for review 

on the Refuge’s CCP website. Public comments were accepted through September 19, 2005. 

 No comments related to this Compatibility Determination were received during the public 

comment period. 

Determination: 

Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations: 

1. The County of San Diego, Department of Environmental Health, Vector Control 

Division shall operate on Refuge lands under the terms and conditions outlined in a 

USFWS Refuge Special Use Permit, which shall be reviewed annually. 

2. Special Use Permit conditions will stipulate that all control work will be carried out 

in conformance with pre-approved USFWS Pesticide Use Proposals, Section 7 

Endangered Species Act consultations, and existing and future USFWS policies on 

mosquito management. 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 8 of 9 

Justification: 

Mosquito management would be implemented on this Refuge in accordance with the 

guidance provided for the Pacific Region by the Regional Office in March 2003. This 

guidance for mosquito management incorporates a phased-response strategy developed to 

manage mosquitoes in a manner that is compatible with refuge purposes and uses the best 

available science while minimizing impacts to fish and wildlife, which is consistent with the 

mission of the National Wildlife Refuge System. Mosquito management proposed for this 

Refuge would also address legitimate human, fish, and wildlife health concerns. 

Implementing mosquito control in accordance with the stipulations presented above would 

therefore not materially interfere with the ability to achieve the wildlife management goals 

established for this Refuge. 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited: 

U.S. Fish and Wildlife Service. 1985. Light-footed Clapper Rail Recovery Plan. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 
 

Final Mosquito Management CD – Sweetwater Marsh Unit 

Page 9 of 9 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 1 of 10 

Compatibility Determination

-FINALUse: Recreational Fishing

Refuge Name: Sweetwater Marsh Unit of the San Diego Bay National Wildlife Refuge 

 (San Diego County, Cities of Chula Vista and National City, California)

 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the Sweetwater Marsh Unit of the San Diego Bay 

National Wildlife Refuge (NWR) are the Endangered Species Act of 1973, as amended (16 

U.S.C. §§1531-1543); Fish and Wildlife Act of 1956, as amended (16 U.S.C. §§742a-742j, 

not including 742d-742l); and the Fish and Wildlife Coordination Act of 1934, as amended 

(16 U.S.C. §§661-667e). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge was established: 

“to protect, manage, and restore habitats for federally listed endangered and 

threatened species and migratory birds, and to maintain and enhance the biological 

diversity of native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species 

Act of 1973, as amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as 

amended); 

”...for the development, advancement, management, conservation, and protection of 

fish and wildlife resources...for the benefit of the United States Fish and Wildlife 

Service, in performing its activities and services. Such acceptance may be subject to 

the terms of any restrictive or affirmative covenant, or condition of servitude...” (Fish 

and Wildlife Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 2 of 10 

Description of Use: 

Recreational fishing is one of the six wildlife dependent recreational uses that should be 

facilitated on a Refuge when determined to be compatible with the Refuge purposes and the 

mission of the National Wildlife Refuge System (System). The public has expressed an 

interest in seeing fishing continue within the south bay, therefore, the potential for 

establishing a fishing program within the Sweetwater Marsh Unit was considered. As 

illustrated in Figure 1-3 of the Final San Diego Bay NWR Comprehensive Conservation Plan 

(CCP)/Environmental Impact Statement (EIS) (USFWS 2006), the areas available for fishing 

within the Sweetwater Marsh Unit are limited to the tidal channels that meander through the 

Refuge’s coastal salt marsh habitat. Currently, these waters are closed to public access, 

including access related to fishing and boating. To facilitate shoreline fishing within the 

Refuge, it would be necessary to permit pedestrian access through coastal salt marsh or along 

the edge of the D Street Fill, as these are the primary areas of the Refuge that abut open 

water. Because of the sensitivity of the marsh habitat and presence of two Federally-listed 

endangered species within the marsh, opening the Refuge to shoreline fishing was not 

evaluated. 

Consideration was given to permitting fishing from non-motorized boats and float tubes 

within the main tidal channel that extends along the south end of the D Street Fill (refer to 

Figure 1-3 of the Final CCP/EIS). The use of motorized vessels was not considered due to 

the shallow depths generally present in the tidal channel. If fishing in this area were to be 

implemented, it would be permitted only during daylight hours and only between midSeptember and the end of January to avoid the nesting season. This proposal assumes no 

launching or landing of boats or float tubes within the Refuge. Existing boat ramps in 

National City and Chula Vista would be available to accommodate visitors. 

Prior to opening the Refuge to this use, regulatory signage would have to be installed at the 

main tidal channel entrances to the Refuge, an information brochure describing fishing 

regulations and sensitive Refuge resources would have be to prepared, and a monitoring and 

periodic fishing line clean-up program would have to be in place. The effects of this activity 

on shorebird foraging and loafing would be monitored twice a month for a period of three 

years. If shorebird activity on the tidal mudflats that border the main tidal channels 

decreases as a result of the introduction of human activity in this area, measures to reduce 

disturbance would have to be implemented. 

Availability of Resources: 

To regulate fishing activities on the Sweetwater Marsh Unit, the following staffing and 

equipment would be required: 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 3 of 10 

Staffing 

Position Involvement FTE Cost 

Project Leader/Deputy 

Project Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.4 $36,400 

Refuge Operations 

Specialist 

Periodic on-site oversight, monitoring of 

fishing and law enforcement activities 0.5 $39,000 

Wildlife Biologist Monitoring, reporting, oversight of 

technician 0.5 $39,000 

Biological Technician Field data collection, assistance with 

monitoring, analysis, and report writing 0.5 $22,750 

Outdoor Recreation 

Planner 

Coordinate the development of a brochure 

describing the fishing opportunities and 

regulations within Sweetwater Marsh 

 0.4 $18,200 

Information and 

Education Specialist 

Assist in design of the brochure and the 

development and implementation of the 

fishing line clean-up program 

 0.2 $15,600 

Law Enforcement Officer Law enforcement 0.5 $31,200 

Park Ranger Assist in Refuge patrol, maintenance, and 

fishing line clean-up program 0.3 $13,000 

Maintenance Worker Install and maintain signs and buoys 0.3 $12,870 

TOTAL FTES AND 

COSTS FOR STAFFING 4.0 $275,720 

Equipment 

Type of Equipment Explanation of Need Cost 

Patrol boat/trailer Needed to patrol refuge waters to ensure 

adherence to Refuge regulations, and to 

monitoring fishing activity 

$50,000 

Signs/Boundary Buoys Needed to delineate the Refuge boundary, 

post regulations, and establish closed areas $10,000 

Create and Print an 

Informational Brochure 

Needed to provide additional information 

about fishing opportunities, rules and 

regulations, wildlife friendly conduct, etc. 

$5,000 

TOTAL COST FOR 

EQUIPMENT $65,000 

Based on the Refuge’s current staffing level, adequate staff to patrol and monitor fishing 

activity on the Refuge is not available to support the proposed use. The coastal refuges 

including Sweetwater Marsh and South San Diego Bay Units and the Tijuana Slough NWR 

currently share one Park Ranger, a Wildlife Biologist, and a Law Enforcement Officer. 

Additional staff time and personnel (including a biological technician, maintenance worker, 

and outdoor recreation planner) would be needed to implement and monitor a fishing 

program on the Refuge. In addition, access to potential fishing areas for monitoring and law 

enforcement patrol would be difficult and time consuming. To provide adequate staff to 

support this use based on the current Refuge budget, the priorities within the current work 

program would have to be reevaluated or staffing levels and the Refuge budget would have 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 4 of 10 

to be increased. 

Implementation of this use would also require approximately $65,000 to purchase a patrol 

boat and trailer, design and print an informational brochure, and produce and install signs 

and buoys in the area proposed for fishing. Adequate funding is available to implement 

periodic clean ups of the area to control trash and discarded fishing line accumulation. 

Anticipated Impacts of the Use: 

DeLong and Schmidt (2000) in their literature review of the effects of human disturbance on 

wildlife summarized the results of a number of studies related to fishing. The majority of 

these studies concluded that fishing activities could influence the composition, distribution, 

abundance, and productivity of waterbirds. Such effects include bird fatalities resulting from 

entanglement with fishing line, trampling of vegetation, degraded habitat due to litter 

accumulation, and reduced water quality due to the deposition of sewage and other 

chemicals. The anticipated impacts of developing a recreational fishing program for this 

Refuge are presented below. 

Endangered and Threatened Species: Human activity associated with fishing and boating 

can have adverse impacts to endangered and threatened species, particularly when this 

activity disrupts nesting or foraging activities. The California least tern (Sternula antillarum) 

and California brown pelican (Pelecanus occidentalis californicus), both Federally-listed 

endangered species, forage within the Refuge’s main tidal channel. In addition, the 

threatened western snowy plover (Charadrius alexandrinus nivosis) forages along the 

channel banks. Potential threats to these species from fishing include disturbance during 

foraging, displacement from preferred feeding areas for prolonged periods, and death from 

entanglement in discarded fishing line. Observations of up to several dead or dying terns 

entangled in one length of fishing line are not unusual within the more dense nesting colonies 

at the South Bay Salt Works. Similar incidents could occur here. The potential for birds to 

become entangled in discarded fishing line could be reduced through public outreach to 

discourage improper disposal of fishing line and periodic cleanup in and along the banks of 

the channel. 

The D Street Fill also supports least tern and western snowy plover nesting. Disturbance 

impacts would be reduced by closing the Refuge to fishing during the nesting season, 

although it is likely that some unauthorized fishing activity may continue to occur during the 

nesting season, potentially resulting in direct impacts to nesting least terns and western 

snowy plovers. 

The endangered light-footed clapper rail (Rallus longirostris levipes) occurs year-round in 

salt marsh and brackish marsh habitats within the Refuge. Threats to this species consist 

primarily of direct habitat or nest losses through trampling of cordgrass or pickleweed that 

could occur if fishing boats are landed along the shoreline or during clean up of trash and 

discarded fishing line. Although clapper rails are not as prone to reacting to the presence of 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 5 of 10 

humans in the vicinity of their habitat as are other species, fishing boats that remain in one 

area for too long could disrupt clapper rail foraging activities. Of equal concern to the health 

and safety of the Refuge’s clapper rail population is the accumulation of discarded fishing 

line along the marsh’s narrow channels. Rails could become entangled in the line and die. 

Trash accumulation resulting from fishing activity in the area could pose a similar threat in 

that predators such as coyotes could be attracted into clapper rail habitat. 

The State endangered Belding’s savannah sparrow (Passerculus sandwichensis beldingi) 

occupies the salt marsh associated vegetation throughout Sweetwater Marsh. Human 

disturbance in these areas could disrupt foraging activities, as well as result in direct habitat 

or nest losses through trampling of pickleweed. This species would also be most directly 

impacted by unauthorized shoreline fishing or landing of fishing boats, permitting access into 

the marsh. Such activity would likely result in vegetation trampling and habitat degradation. 

In addition to endangered and threatened bird species, the Sweetwater Marsh Unit also 

supports the Federally-listed endangered annual plant species, salt marsh bird’s beak 

(Cordylanthus maritimus maritimus). The salt marsh bird’s beak is distributed in various 

locations throughout the marsh, primarily in upper marsh elevations that are inundated by 

tides on a regular basis, but above areas that receive daily salt water flooding. Such areas are 

more likely to be impacted by unauthorized pedestrian access, because they are drier than 

other portions of the marsh. Yearly population numbers depend directly on seed dispersal 

and successful plant establishment. Field observations indicate that even a moderate amount 

of foot traffic can damage the fragile seedlings (USFWS 1985), resulting in decreased 

population numbers. Therefore, unauthorized shoreline fishing or landing of fishing boats 

along the shoreline could result in direct impacts to this species. Fishing line cleanups could 

also result in impacts to this species. 

Sensitive Habitats: Recreational fishing within the Sweetwater Marsh Unit would introduce 

human activity into the center of the Refuge and permit boating activity in proximity to 

sensitive wetland habitat, creating the potential for direct and indirect impacts to sensitive 

habitat. These impacts could involve trampling of vegetation, disturbance to tidal mudflats, 

possible damage to cordgrass habitat, and increased erosion along the shore. 

Migratory Birds: The Sweetwater Marsh Unit provides essential habitat for avian species 

migrating along the Pacific Flyway. The coastal salt marsh within the Refuge, with its many 

interconnecting channels, provides important resting and feeding areas for many migratory 

birds. Common wintering and migrating birds include long-billed curlew (Numenius 

americanus), whimbrel (Numenius phaeopus) and willet (Catoptrophorus semipalmatus). 

The extensive mudflats that occur immediately to the west of the D Street Fill, outside the 

Refuge boundary, also provide important habitat for these and other migratory birds. 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 6 of 10 

A study of the effects of watercraft on foraging and resting birds in San Diego Bay reported 

that all watercraft, including motorized boats and non-motorized boats, result in some level 

of disturbance to waterbirds (Huffman 1999). Observations made during the study indicate 

that when a boat approaches the shoreline, waterfowl located between the boat and shore and 

any shorebirds along the shoreline are flushed regardless of the speed of the watercraft. 

Huffman noted that when non-motorized vessels, including rowboats, kayaks, canoes, and 

longboats, came within 30 meters of the shoreline all waterfowl between the craft and the 

shore would flush. At the widest point, the channels within the Sweetwater Marsh are 

approximately 20 meters in width. Therefore, as a fishing boat moves through the channel, 

any birds foraging or resting on the tidal mudflats adjacent to the channel would be flushed. 

These birds would then be forced to move to another location in the general vicinity. 

Frequent disturbance to foraging and loafing shorebirds could occur depending upon the 

number of boats using the channel on a given day. Such disturbance would reduce an 

individual bird’s ability to meet its energy requirements, while also causing the bird to 

expend energy in the process of flying away from the disturbance. If disturbance becomes to 

frequent, those birds that do not habituate could permanently leave the area (West et al. 

2002). Increasing the intensity of boating activity in the vicinity of the mudflats immediately 

to the west of Gunpowder Point could also result in cumulative impacts to the migratory 

shorebirds that forage in proximity to the Refuge. 

 

Huffman also documented disturbance to migratory birds as a result of pedestrian activity 

along the shoreline. This disturbance was greatest during low tides when pedestrians left 

designated accessways to explore the mudflats. This activity affected both shorebirds and 

waterfowl. Huffman observed that human activity along the shoreline and in the mudflats 

would flush all birds within a 50 to 100 meter radius. Based on these observations, it is 

assumed that if fishing were to be permitted along the shoreline on Refuge lands, the 

availability of habitat for migratory birds could be reduced. This is because the presence of 

anglers along the shoreline would cause most birds to avoid those habitats located as much as 

100 meters away from the fishermen. 

Migratory birds could also experience injury or death as a result of discarded fishing line. 

Once a bird becomes entangled in fishing line, it generally dies. Many bird deaths have been 

attributed to fishing line entanglement within the south bay. 

 

Nesting Season Disturbance: The nesting season varies with individual species, but can 

generally be described as occurring between mid-February and mid-September. Nesting 

occurs within the Refuge’s salt marsh habitat, as well as on D Street Fill. Several ground 

nesting avian species utilize the bare areas of the D Street Fill including the endangered 

California least tern and the threatened western snowy plover. Forster’s terns (Sterna 

forsteri) also periodically nest in this area. Nesting activity on D Street Fill generally occurs 

from mid-April through mid-September. 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 7 of 10 

Disturbance to nesting bird species may occur if persons are present in the vicinity of avian 

nesting colonies or individual nests. Biologists performing nesting surveys on the South San 

Diego Bay Unit report that nesting seabirds responded to human activity occurring at some 

distance from the colony. Similar disturbance patterns would be expected at D Street Fill. In 

general, avian responses to disturbance can include flocking, alarm calling, nest 

abandonment, colony abandonment, and inter-colony antagonistic behaviors leading to 

crushed eggs and killed chicks. Predatory species, particularly avian species such as 

northern harrier, ravens, and crow, may also use disturbance episodes to depredate eggs and 

chicks while the adults are flocking or otherwise distracted. Disturbance to nesting birds 

from activities associated with fishing and boating can occur in several ways: disturbance 

from vessels located too close to the shoreline and disturbance from human encroachment 

into nesting areas when watercraft are landed along the shore. Human disturbance near 

nesting grounds has been identified as a primary limiting factor for seabird reproductive 

productivity in nesting areas with urban interfaces. By closing the Refuge to fishing during 

the nesting season, such impacts could be reduced. However, occasional monitoring and 

enforcement actions would likely be required during the closure, which could result in 

disturbance to nesting birds. 

The Federal endangered light-footed clapper rail and State endangered Belding’s savannah 

sparrow nest in Refuge’s salt marsh vegetation, which abuts the main tidal channel. Nesting 

generally occurs from mid-February to mid-September. The primary threats to nesting these 

species from recreational fishing would occur if unauthorized fishing occurs from the 

shoreline or fishing boats are landed and fishermen enter sensitive nesting habitat along the 

edges of the marsh. As described above, such impacts could be minimized, although 

probably not avoided, by closing the Refuge to fishing during the nesting season. Clapper 

rail chicks could also be directly or indirectly impacted by the accumulation of trash and 

discarded fishing line in the marsh. 

Public Review and Comment:

Recreational fishing has been discussed on several occasions at public workshops held in 

conjunction with the CCP process. To initiate this process, a Notice of Intent was published 

in the Federal Register on June 23, 2000 (65 FR 39172). At that time, written comments 

were solicited. In July 2000, two initial scoping meetings were held, one in Imperial Beach 

and one in Chula Vista, to receive input from the public on issues related to the San Diego 

Bay NWR. Due to the public’s level of interest in these refuges, focused public workshops 

were held in September 2000 and June 2001 to specifically address the issue of public use. 

Three additional workshops were held between November 2000 and May 2001 to receive 

input from the public on wildlife management and restoration proposals for these refuges. 

All of the public meetings were well attended with at least 40 people present at each meeting. 

 Approximately 50 to 60 people attended those meetings related to public use. 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 8 of 10 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. One of these updates was devoted entirely to the topic of 

public use. These Planning Updates have been distributed to more than 1,000 individuals 

and organizations representing interested members of the public, conservation organizations, 

hunting, fishing and boating organizations, public agencies, municipalities, special districts, 

Tribes, and adjoining property owners. We received more than 50 letters, emails, and phone 

calls related to public use between June and November 2001 and numerous other 

communications relevant to public uses on the Refuge were received in 2002 and 2003. 

The public provided a range of written and verbal comments related to fishing. These 

comments included requests to permit fishing within the Sweetwater Marsh and South San 

Diego Bay Units and to manage the refuge ecosystems for fish, prohibit fishing within both 

refuges, permit the use of low power motorized boats to accommodate fishing, and clearly 

define fishing and non-fishing areas if fishing is permitted on each refuge. Although most 

comments related to fishing from boats, there was a request to provide access along the 

shoreline to accommodate fishing for non-boat owners. Several individuals also expressed 

concerns regarding the adverse affects that discarded fishing line can have on seabirds. 

The draft Compatibility Determination for recreational fishing on the Sweetwater Marsh Unit 

was circulated for public review and comment as part of the San Diego Bay National 

Wildlife Refuge draft CCP/EIS. Specifically, it was included in Appendix K of the draft 

CCP/EIS. The Notice of Availability for the draft CCP/EIS was published in the Federal 

Register on July 22, 2005 and a Planning Update announcing the availability of the draft was 

sent to over 1,000 individuals, agencies, non-governmental organizations, and other 

stakeholders. In addition, the draft CCP/EIS was provided to over 275 interested parties and 

made available for review on the Refuge’s CCP website. Public comments were accepted 

through September 19, 2005. No comments related to this Compatibility Determination were 

received during the public comment period. 

Determination: 

 X Use is Not Compatible 

 Use is Compatible with the Following Stipulations 

Justification:

The salt marsh complex within the Sweetwater Marsh Unit is the largest remaining coastal 

salt marsh within San Diego Bay, and as such it provides regionally significant habitat for 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 9 of 10 

numerous migratory shorebirds. Further, this is one of only a few places in San Diego 

County that provides suitable habitat for the Federally-listed endangered light-footed clapper 

rail. It is for these reasons that the Sweetwater Marsh Unit was established. The Refuge 

purposes include conserving fish and wildlife which are Federally-listed as endangered or 

threatened species and managing, conserving, and protecting fish and wildlife resources. 

After evaluating the anticipated impacts of implementing a recreational fishing program on 

the Sweetwater Marsh Unit, the Refuge Manager has determined that opening a portion of 

the Refuge to recreational fishing would materially interfere with one of the primary Refuge 

purposes, “to conserve endangered and threatened species.” The only areas available within 

the Refuge for fishing are the relatively narrow channels that flow through the existing 

coastal marsh habitat. The edges of these marsh channels provide important foraging and 

resting habitat for migratory birds and several listed species, including the light-footed 

clapper rail, one of the rarest avian species in California, and the western snowy plover. If 

fishing were permitted in these channels, direct and indirect impacts to clapper rails and their 

habitat could occur, which would be in direct conflict with Refuge’s current endangered 

species management efforts. In addition to potential impacts to listed species, introducing 

this use into the center of the Refuge would result in disturbance impacts to migratory birds 

potentially displacing those shorebirds and seabirds that forage along the main tidal channel 

within the marsh. These effects would materially interfere with the mission of the National 

Wildlife Refuge System. 

Due to the sensitivity of the area available to accommodate the recreational fishing on this 

Refuge, it is not possible to facilitate a recreational fishing program and still achieve the 

Refuge’s endangered species and coastal wetland protection goals. In addition, to implement 

this proposal would require the identification of additional funds to cover the cost of 

materials and staff to monitor this activity. The reallocation of staffing priorities to 

implement this use would necessarily interfere with the Refuge’s ability to implement 

wildlife dependent recreational uses such as environmental education and interpretation that 

are currently occurring on the Refuge. The affects of implementing this proposal would 

therefore be contrary to the Refuge goal of providing opportunities for wildlife-dependent 

recreational uses that are compatible with refuge purposes and foster a broader understanding 

the value of, and need for, wildlife conservation. 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 
 

Final Recreational Fishing CD – Sweetwater Marsh Unit 

Page 10 of 10 

References Cited:

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance 

on Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater 

National Wildlife Refuge (Draft). 

Huffman, Kathy. 1999. San Diego South Bay Survey Report – Effects of Human Activity 

and Water Craft on Wintering Birds in the South San Diego Bay. 

U.S. Fish and Wildlife Service. 1985. Salt Marsh Bird’s Beak (Cordylanthus maritimus

maritimus) Recovery Plan. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 

West, A. D., J. D. Goss-Custard, R. A. Stillman, R. W. G. Caldow, S. E. A. le V. dit Durell 

and S. McGrorty. 2002. Predicting the impacts of disturbance on shorebird mortality using a 

behaviour-based model. Biological Conservation 106:319-328. 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 1 of 11 

Compatibility Determination

-FINALUse: Interpretive Water Trail (Recreational Boating) 

Refuge Name: Sweetwater Marsh Unit of the San Diego Bay National Wildlife Refuge 

 (San Diego County, Cities of Chula Vista and National City, California) 

 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the Sweetwater Marsh Unit are the Endangered 

Species Act of 1973, as amended (16 U.S.C. §§1531-1543); Fish and Wildlife Act of 1956, 

as amended (16 U.S.C. §§742a-742j, not including 742d-742l); and the Fish and Wildlife 

Coordination Act of 1934, as amended (16 U.S.C. §§661-667e). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge (NWR) was established: 

“to protect, manage, and restore habitats for federally listed endangered and 

threatened species and migratory birds, and to maintain and enhance the biological 

diversity of native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species 

Act of 1973, as amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as 

amended); 

”...for the development, advancement, management, conservation, and protection of 

fish and wildlife resources...for the benefit of the United States Fish and Wildlife 

Service, in performing its activities and services. Such acceptance may be subject to 

the terms of any restrictive or affirmative covenant, or condition of servitude...” (Fish 

and Wildlife Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 2 of 11 

Description of Use: 

Currently the waters of the Sweetwater Marsh Unit are closed to public access including any 

form of boating. During the September 2000 public workshop for the Sweetwater Marsh and 

South San Diego Bay Units of the San Diego Bay NWR Comprehensive Conservation Plan 

(CCP), the public expressed a desire to see an interpretive water trail developed through the 

Sweetwater Marsh for kayaks and canoes. As a result, such a proposal was considered 

during the development of alternatives for the CCP. Water trails and boating are not 

identified as wildlife dependent recreational uses, however, these uses would facilitate 

wildlife observation and photography and environmental interpretation, three of the six 

priority public uses that should be facilitated on a Refuge when determined to be compatible 

with the purpose of the Refuge and the mission of the System. 

The development of an interpretive water trail on this Refuge would require that a portion of 

tidal channels within the Refuge be opened to boating. Due to the limited width and depth of 

the water channels within Sweetwater Marsh, only non-motorized, paddle-type vessels, such 

as kayaks and canoes, would be permitted to use the water trail. All other types of boats 

would be prohibited. This analysis assumes that non-motorized vessels would only be 

permitted to travel along a specific designated trail route; all other water areas of the Refuge 

would continue to be closed to public access. The trail route, which would be illustrated on 

signs placed at the two water entrances to the Refuge and delineated through small buoys, 

water markers, and/or signs, would begin in the Sweetwater flood control channel to the 

south of the point where the Paradise Marsh tidal channel enters the flood control channel 

(refer to Figure 2-1 in the Final CCP/EIS). From here, the trail would travel south through 

the connector marsh to its convergence with the historic Sweetwater River channel, then the 

trail would turn to the west. The trail would then continue west along the old river channel 

to the point where the channel reenters the Bay. 

It is assumed that use of the interpretive water trail would be permitted daily from sunrise to 

sunset, although users would be encouraged to avoid periods of low tide when the water 

levels would be too shallow to permit easy navigation through the tidal channel. The trail 

would be closed during the nesting season (between mid-February through mid-September) 

to minimize disturbance to birds nesting on the D Street Fill. Prior to opening the Refuge to 

this use, regulatory signage would have to be installed at the water entrances to the Refuge 

and a monitoring program would have to be in place. Periodic monitoring of the effects of 

human activity on shorebird foraging and loafing would be necessary to ensure that no 

adverse effects to migratory birds were occurring. 

 

Even if non-motorized boat use were to be permitted in the Refuge, the launching and 

landing of watercraft within the Refuge would be prohibited at all times. Watercraft would 

have to be launched from one of the existing boat launches to the north or south of the 

Refuge. Because this trail would travel through sensitive habitat that supports the Federal 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 3 of 11 

endangered light-footed clapper rail (Rallus longirostris levipes), as well as numerous 

species of shorebirds, it would likely be necessary to implement a reservation system to limit 

the number of boats or groups of boats traveling through the area per week. The number of 

disturbances that could occur within this area without adversely affecting the rails and other 

birds supported by the surrounding tidal mudflats and salt marsh habitat would have be 

determined through a monitoring program. 

To implement this use, the general route of the trail would have to be delineated with buoys 

and/or water markers and the tidal channels branching off from the main channel would have 

to be marked as closed. In addition, an interpretive pamphlet or brochure would be 

developed that would include a map of the trail route, rules and regulations to be followed 

while using the trail, and a description of the reservation system and how to reserve a time to 

use the trail. This information would be made available at the Chula Vista Nature Center, 

Refuge offices within the San Diego NWR Complex, and other appropriate locations. The 

information would also be provided on the Complex’s website. 

Availability of Resources: 

To implement an interpretive water trail and regulate and monitor the activities associated 

with the use of the trail, the following staffing and equipment would be required: 

Staffing 

Position Involvement FTE Cost 

Project Leader/Deputy 

Project Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.4 $36,400 

Refuge Operations 

Specialist 

Periodic on-site oversight, assist in the 

development of a reservation system, 

monitor law enforcement activities 

0.5 $39,000 

Wildlife Biologist Assist in design of the trail, prepare and 

implement a monitoring plan to evaluate 

disturbance impacts, supervise bio tech 0.5 $39,000 

Biological Technician Field data collection, assistance with 

monitoring, analysis, and report writing 0.5 $22,750 

Information and 

Education Specialist 

Coordinate design of informational 

pamphlet and update website, assist in 

the development of a reservation system 

0.3 $23,400 

Outdoor Recreation 

Planner 

Design the water trail and assist in 

siting of buoys and regulatory signs 

0.5 $22,750 

Park Ranger Implement the reservation system, 

install and maintain buoys, water 

markers, and signs along the trail, 

monitor trail use 

0.3 $13,000 

Law Enforcement Officer Law enforcement 0.5 $31,200 

TOTAL FTES AND 

COSTS FOR STAFFING 3.9 $275,200 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 4 of 11 

Equipment 

Type of Equipment Explanation of Need Cost 

Buoys, water trail 

markers, and signs 

Buoys or water trail markers are needed to 

mark the alignment of the water trail; 

signs would illustrate the trail route, 

inform uses of closed areas, and provide 

general information about rules and 

regulations 

$20,000 

Patrol Boat/Trailer Needed to patrol refuge waters for 

enforcement of Refuge regulations, 

monitoring, and safety related issues 

$50,000 

Information Pamphlet Design, layout, and printing of an 

information pamphlet or brochure to 

illustrate the trail route, present rules and 

regulations, and provide interpretive 

information about the resources along the 

trail 

$5,000 

TOTAL COST FOR 

EQUIPMENT $75,000 

Refuge staff availability is critical to the implementation and administration of a seasonal 

interpretive water trail within the Sweetwater Marsh Unit due to the biological significance 

of the area in which the use is proposed. Based on the Refuge’s current staffing level, 

adequate staff is not available to support the proposed use. The coastal refuges including 

Sweetwater Marsh and South San Diego Bay Units and the Tijuana Slough NWR currently 

share one Park Ranger, a Wildlife Biologist, and a Law Enforcement Officer. Additional 

staff time would be needed to monitor and patrol the proposed interpretive trail, requiring 

either a reassessment of the current work program to change priorities or an increase in 

current staffing levels to support the use. Implementation of this use would also require 

approximately $20,000 to purchase buoys, water markers, and signs needed to delineate the 

water trail and post closed areas and to design and print an informational pamphlet for the 

trail. An additional $50,000 would be required to purchase a patrol boat and trailer to 

facilitate patrol and monitoring of boating activity within the Refuge. 

Although funding may be identified through Federal cost share grants, local or state grants, 

or contributions to the Refuge’s Friends Group to purchase required materials, the lack of 

adequate staffing to implement the program could only be resolved through an increase in the 

current Refuge budget. 

The proposal to open a portion of the Refuge waters to accommodate an interpretive water 

trail would not require any funds to develop boat ramps or other boating-related facilities as 

they would not be constructed within the Refuge. Adequate accommodations for such 

facilities are provided just outside the Refuge boundary in Chula Vista and Coronado. 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 5 of 11 

Anticipated Impacts of the Use: 

The effects of human disturbance on waterfowl and wintering birds have been the subject of 

numerous studies (DeLong and Schmidt 2000). These studies indicate that the degree of 

disturbance varies depending upon the use (Korschgen and Dahlgren 1992) and that boating 

activity can cause foraging and loafing shorebirds to flush if the activity occurs too close to 

the shoreline (Huffman 1999). The potential affects of introducing human activity into the 

marsh to accommodate an interpretive water trail are summarized below. 

Migratory Birds: The Sweetwater Marsh Unit provides important habitat for avian species 

migrating along the Pacific Flyway. The Refuge’s coastal salt marsh, with its many 

interconnecting channels and adjacent tidal mudflats, provide important foraging and resting 

areas for many wintering and migrating shorebirds and waterfowl. Some of the most 

common of these species include the long-billed curlew (Numenius americanus), whimbrel 

(Numenius phaeopus) and willet (Catoptrophorus semipalmatus). 

In an effort to characterize species richness, relative abundance, and spatial distribution of 

the waterbird community in central and south San Diego Bay, waterbird surveys were 

conducted in South San Diego Bay between April 15, 1993 and April 14, 1994 (USFWS 

1995). According to the report, “a mean of 6,981 birds were observed each visit during peak 

winter months (November through February).” In describing the locations of waterbird 

occurrences throughout central and south San Diego Bay, the report states that, “areas with 

relatively low water recreational intensity supported a greater abundance of waterbirds.” 

Between January and March 1998, a study was conducted to observe the effects of watercraft 

on wintering birds in the southern end of San Diego Bay (Huffman 1999). The study, which 

was prepared for the Fish and Wildlife Service, was designed to observe and record the 

effects of human disturbance, particularly disturbances related to watercraft, on wintering 

birds in the bay. During the study, Huffman observed that operating any watercraft, 

including motorized boats, non-motorized boats, jet skis, wind surfers, and parasails, within 

the Bay resulted in some level of disturbance to waterbirds. The degree of disturbance 

depended upon the vessel’s speed, proximity to rafting birds, proximity to the shoreline, and 

amount of noise produced during operation. Of all the types of watercraft used in the bay, 

Huffman observed that powerboats resulted in the greatest disturbances to the avian 

community. Huffman also noted that disturbance to birds was greatly reduced when boats 

traveled at the posted “No Wake” speed (5 mph). 

Other observations made by Huffman included the effect that watercraft had on shorebirds 

foraging along the edge of the bay. Huffman reports that in cases in which motorized 

watercraft were within 100 meters off the shore, all waterfowl between the boat and shore 

and any shorebirds along the shoreline would flush regardless of the speed of the watercraft. 

Similarly, when non-motorized vessels, including kayaks, canoes, and longboats, came 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 6 of 11 

within 30 meters of the shoreline all waterfowl between the craft and the shore would flush 

to another portion of the bay. The approximate width of the tidal channels that would be 

included within the water trail route is 20 meters, therefore, based on the results of 

Huffman’s observations; frequent disturbance to foraging and loafing shorebirds would be 

expected as a result of the proposed boating. Such disturbance can reduce an individual 

bird’s ability to meet its energy requirements by causing the bird to expend energy in the 

process of flying away from the disturbance. If disturbance becomes to frequent, those birds 

that do not habituate could permanently leave the area (West et al. 2002). Increasing the 

intensity of boating activity in the vicinity of the mudflats immediately to the west of 

Gunpowder Point could also result in cumulative impacts to the migratory shorebirds that 

forage in proximity to the Refuge. 

Endangered and Threatened Species: One of the purposes for the establishment of the 

Sweetwater Marsh Unit is to protect Federally-listed endangered or threatened species. 

Human activity can have adverse impacts on endangered and threatened species, particularly 

when this activity disrupts bird nesting or foraging. The California least tern (Sternula 

antillarum) and California brown pelican (Pelecanus occidentalis californicus), both 

Federally-listed endangered species, forage within the main tidal channel within the 

Sweetwater Marsh, while the threatened western snowy plover (Charadrius alexandrinus 

nivosis) forages year round along the channel banks. The D Street Fill portion of the Refuge 

also supports least tern and western snowy plover nesting. Increasing human activity within 

the Refuge’s main tidal channel could disrupt current foraging patterns for these species, and 

possibly displace these species to other less productive portions of the Refuge. 

The Federal endangered light-footed clapper rail also occurs within Sweetwater Marsh Unit 

in the Refuge’s salt marsh and brackish marsh habitats. Threats to the light-footed clapper 

rail consist primarily of direct habitat or nest losses through trampling of cordgrass or 

pickleweed. Such impacts would occur if boats were landed along the channel banks and 

unauthorized intrusion into the marsh was to occur. Clapper rails are also at risk because 

they are slower to react to the presence of humans in the vicinity of their habitat as are other 

bird species; therefore, they are more vulnerable to injury and death from human intrusion. 

The introduction of human activity along the Refuge’s primary tidal channel could indirectly 

impact the Refuge’s rail population by forcing the birds to relocate away from the main areas 

of disturbance. Because the main tidal channel is located near the center of the Refuge, the 

rails would actually be relocating closer to the edges of the Refuge where the chances for 

predation would be greater. The potential affects to clapper rails of introducing human 

activity into the marsh would be contrary to the objectives of the Light-footed Clapper Rail 

Recovery Plan (USFWS 1985a). Specifically, the Plan’s primary objective is to increase the 

rail breeding population by providing adequately protected, suitably managed, secure 

wetland habitat. Some of the recommendations included in the Recovery Plan include 

protecting existing habitat, controlling human disturbance in clapper rail areas, and 

increasing the carrying capacity and stability of existing habitat. 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 7 of 11 

 

The State endangered Belding’s savannah sparrow (Passerculus sandwichensis beldingi) 

occupies the high salt marsh vegetation throughout Sweetwater Marsh. Human intrusion into 

these areas could disrupt foraging activities, as well as result in direct habitat or nest losses 

through trampling of pickleweed. This species would also be most directly impacted by 

unauthorized access into the marsh from boats that have landed on the shoreline. Such 

activity would likely result in vegetation trampling and habitat degradation. 

In addition to endangered and threatened bird species, the Sweetwater Marsh Unit also 

supports the Federally-listed endangered annual plant species, salt marsh bird’s beak 

(Cordylanthus maritimus maritimus). Salt marsh bird’s beak is distributed in various 

locations throughout the marsh, primarily in upper marsh elevations that are inundated by 

tides on a regular basis, but above areas that receive daily salt water flooding. Such areas are 

more likely to be impacted by unauthorized pedestrian access, because they are drier than 

other portions of the marsh. Yearly population numbers depend directly on seed dispersal 

and successful plant establishment. Field observations indicate that even a moderate amount 

of foot traffic can damage the fragile seedlings (USFWS 1985b), resulting in decreased 

population numbers. Therefore, the unauthorized landing of boats along the edges of the 

marsh’s main channel could result in direct impacts to this species. 

 

Nesting Season Disturbance: Human disturbance to nesting birds from activities associated 

with watercraft can occur in several ways: disturbance from the vessel itself due to 

encroachment on the shoreline and disturbance from human encroachment into nesting areas 

when watercraft are landed along the shore. Huffman (1999) observed bird flushing when 

motorized watercraft came within 100 meters of the shoreline and non-motorized vessels 

came within 30 meters of the shoreline. Similar effects to nesting seabirds would be 

expected. When a kayaker landed along the shore of the Chula Vista Wildlife Reserve, a 

habitat mitigation area created by the Unified Port of San Diego that is located just to the 

north of the salt works in the southern end of San Diego Bay, Huffman noted that the 

remaining shorebirds and other upland birds in the area flushed. Such human disturbance on 

the nesting grounds has been identified as a primary limiting factor for seabird reproductive 

productivity in nesting areas with urban interfaces. 

Disturbance to nesting migratory bird species may occur if a watercraft is present in the 

vicinity of a nesting colony or individual nests. Several species, many of which are rare, 

sensitive or state and/or Federally-listed, nest on the relatively bare ground at D Street Fill, as 

well as in vegetated habitats within Sweetwater Marsh. The Belding’s savannah sparrow 

nests in salt marsh associated vegetation throughout Sweetwater Marsh, while the 

endangered California least tern and threatened western snowy plover nest at D Street Fill. 

Biologists performing nesting surveys at the salt works on the South San Diego Bay Unit 

report that seabird colonies will respond to pedestrian traffic. These responses vary with 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 8 of 11 

date, nature of disturbance and other unknown factors. Avian responses to disturbance can 

include flocking, alarm calling, nest abandonment, colony abandonment and inter-colony 

antagonistic behaviors leading to crushed eggs and killed chicks. Predatory species, 

particularly avian predators such as northern harrier, common raven, American crow, and 

some gull species, may also use disturbance episodes to depredate eggs and chicks while the 

adults are flocking or otherwise distracted. Closing the water trail during the nesting season 

would reduce these types of disturbance impacts, however, enforcement of the nesting season 

closure could be difficult once the public becomes accustom to the trail being open during 

much of the year. Opening the water trail only to those with a reservation could help in the 

process of informing the public about when and how the proposed trail can be used. 

Public Review and Comment: 

The development of water trails to facilitate wildlife dependent recreational uses was 

discussed on several occasions at public workshops held in conjunction with the 

Comprehensive Conservation Plan (CCP) process. To initiate the CCP process, a Notice of 

Intent was published in the Federal Register on June 23, 2000 (65 FR 39172). At that time, 

written comments were solicited. In July 2000, two initial scoping meetings were held, one 

in Imperial Beach and one in Chula Vista, to receive input from the public on issues related 

to the Sweetwater Marsh and South San Diego Bay Units. Due to the public’s level of 

interest in these refuges, focused public workshops were held in September 2000 and June 

2001 to specifically address the issue of public use. Three additional workshops were held 

between November 2000 and May 2001 to receive input from the public on wildlife 

management and restoration proposals for these refuges. All of the public meetings were 

well attended with at least 40 people present at each meeting. Approximately 50 to 60 

people attended those meetings related to public use. 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. One of these updates was devoted entirely to the topic of 

public use. These Planning Updates have been distributed to more than 1,000 individuals 

and organizations representing interested members of the public, conservation organizations, 

hunting, fishing and boating organizations, public agencies, municipalities, special districts, 

Tribes, and adjoining property owners. We received more than 50 letters, emails, and phone 

calls related to public use between June and November 2001 and numerous other 

communications relevant to public uses on the Refuge were received in 2002 and 2003. 

The draft Compatibility Determination for a water trail through the Sweetwater Marsh Unit 

was circulated for public review and comment as part of the San Diego Bay National 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 9 of 11 

Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental Impact Statement 

(CCP/EIS). Specifically, it was included in Appendix K of the draft CCP/EIS. The Notice 

of Availability for the draft CCP/EIS was published in the Federal Register on July 22, 2005 

and a Planning Update announcing the availability of the draft was sent to over 1,000 

individuals, agencies, non-governmental organizations, and other stakeholders. In addition, 

the draft CCP/EIS was provided to over 275 interested parties and made available for review 

on the Refuge’s CCP website. Public comments were accepted through September 19, 2005. 

 No comments related to this Compatibility Determination were received during the public 

comment period. 

Determination: 

 X_Use is Not Compatible 

 _ _Use is Compatible with the Following Stipulations 

Justification:

After evaluating the anticipated impacts of implementing an interpretive water trail on the 

Sweetwater Marsh Unit, the Refuge Manager has determined that allowing this use would 

materially interfere with one of the primary purposes of this Refuge, which is “to conserve 

endangered and threatened species.” The introduction of human activity within the main 

portion of the marsh would impede the foraging and nesting activities of the light-footed 

clapper rail and could potentially disrupt foraging activity of the western snowy plover. The 

proposed activity would also result in frequent disturbance to shorebirds that forage and rest 

on the tidal mudflats along the main tidal channel in the marsh. These impacts would be 

contrary to the wildlife conservation mission of the National Wildlife Refuge System. The 

affects of implementing this proposal would therefore be contrary to the Refuge goal of 

providing opportunities for wildlife-dependent recreational uses that are compatible with 

refuge purposes and foster a broader understanding the value of, and need for, wildlife 

conservation. 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 10 of 11 

References Cited: 

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance on 

Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater National 

Wildlife Refuge (Draft). 

Huffman, Kathy. 1999. San Diego South Bay Survey Report – Effects of Human Activity and 

Water Craft on Wintering Birds in the South San Diego Bay. 

Korschgen, Carl and Robert Dahlgren. 1992. Human Disturbances of Waterfowl: Causes, 

Effects, and Management. 

U.S. Fish and Wildlife Service. 1985a. Light-footed Clapper Rail Recovery Plan. 

U.S. Fish and Wildlife Service. 1985b. Salt Marsh Bird’s Beak (Cordylanthus maritimus subsp. 

maritimus) Recovery Plan. 

U. S. Fish and Wildlife Service. 1995. Waterbirds of Central and South San Diego Bay 1993-

1994. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 

West, A. D., J. D. Goss-Custard, R. A. Stillman, R. W. G. Caldow, S. E. A. le V. dit Durell 

and S. McGrorty. 2002. Predicting the impacts of disturbance on shorebird mortality using a 

behaviour-based model. Biological Conservation 106:319-328. 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 
 

Final Interpretive Water Trail CD – Sweetwater Marsh Unit 

Page 11 of 11 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 1 of 10 

Compatibility Determination

-FINALUse: Wildlife Observation and Photography

Refuge Name: South San Diego Bay Unit of the San Diego Bay National Wildlife Refuge 

(San Diego County, Cities of Coronado, Chula Vista, Imperial Beach, 

National City, and San Diego, California) 

Establishing and Acquisition Authorities:

The authorities for the establishment of the San Diego National Wildlife Refuge are the Fish 

and Wildlife Act of 1956, as amended (16 U.S.C. 742a-742j, not including 742d-742l), and 

the Endangered Species Act of 1973, as amended (16 U.S.C. 1531-1543). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge was established: 

“to protect, manage, and restore habitats for federally listed endangered and threatened 

species and migratory birds, and to maintain and enhance the biological diversity of 

native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species Act of 1973, as 

amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as amended); 

”...for the development, advancement, management, conservation, and protection of fish 

and wildlife resources...for the benefit of the United States Fish and Wildlife Service, in 

performing its activities and services. Such acceptance may be subject to the terms of 

any restrictive or affirmative covenant, or condition of servitude...” (Fish and Wildlife 

Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 2 of 10 

Descriptions of Use: 

At present, the primary opportunities for wildlife observation and photography from within 

the Refuge boundary are available via watercraft in the open waters of the Refuge or 

immediately adjacent to the Refuge along the Bayshore Bikeway. Opportunities for the 

public to observe wildlife from within the salt works are also available via guided tours. 

At the scoping meetings for the Comprehensive Conservation Plan (CCP), as well as at 

subsequent public use workshops held in September 2000 and June 2001, the public 

expressed an interest in expanding opportunities for wildlife observation and photography 

within the South San Diego Bay Unit. As described in the Public Use Program discussion in 

Section 2.3.2.4 of the Final CCP/Environmental Impact Statement (EIS) for the South San 

Diego Bay Unit (USFWS 2006), the CCP includes several proposals for expanding 

opportunities for these uses including: 

1. Increasing the number of guided tours provided of the salt works between midSeptember and early February of each year to about two per month; 

2. Establishing observation points on the north side of the Bayshore Bikeway: at the 

northern terminus of 10th Street, at the northern terminus of 8th Street, and in the 

vicinity of Florida Street in Imperial Beach. From these areas, the wildlife activities 

occurring in the river channel and Ponds 22, 23, and 10 can be observed (refer to 

Figure 2-14 of the Final CCP/EIS);and 

3. Establishing an observation area along the eastern edge of Pond 29 in the City of 

Chula Vista, where views of the northeastern pond system could be provided (refer to 

Figure 2-14 of the Final CCP/EIS). 

An elevated platform was also proposed near 13th Street in the draft CD, however, upon 

further analysis, it was determined that this structure was not needed to achieve the goals for 

wildlife observation and photography. The existing elevations to the north of the bikeway in 

the vicinity of Florida Street are high enough to allow for observations of avian activities 

within the salt ponds without the need for an elevated platform. As a result, the elevated 

platform has been replaced with a proposal to construct an overlook area on a knoll to the 

north of the Bayshore Bikeway and the northeast of the terminus of Florida Street. 

The observation areas proposed around the perimeter of the Refuge would be accessible from 

the Bayshore Bikeway and several public streets in northern Imperial Beach. A parking area 

that serves users of the Bayshore Bikeway is available at the northern terminus of 13th Street 

and on-street parking is available along Florence Street, 8th Street, and Boulevard Avenue. 

The City of Imperial Beach also proposes to construct a new parking area at the terminus of 

10th Street. Based on preliminary concepts for the observation areas, the design would be 

relatively informal, consisting of a leveled area with a hardened surface of stabilized soil or 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 3 of 10 

decomposed granite. A post and cable fence or other appropriate barrier would be provided 

at the northern edge of the observation areas to minimize disturbance to adjacent vegetation. 

These observation areas would also include interpretive elements as described in the 

Compatibility Determination for environmental education and interpretation for this Unit. 

A reservation system would be established in association with the expansion of the salt 

works guided tour program, as these tours would be limited to approximately 15 people per 

tour. About two tours per month would be conducted between mid-September and midFebruary. No tours would be provided during the breeding season to avoid disturbance to 

nesting birds. 

Availability of Resources: 

To implement and administer opportunities for wildlife observation and photography, the 

following staffing and materials/facilities would be required: 

Staffing 

Position Involvement FTE Cost 

Project Leader/Deputy 

Project Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.3 $27,300 

Refuge Operations 

Specialist 

Periodic on-site oversight, monitoring of 

law enforcement activities 0.4 $31,200 

Wildlife Biologist Monitoring, reporting, assistance in the 

design and siting of overlook areas and 

oversight in their implementation, 

oversight of bio tech; assist in conducting 

tours 

0.5 $39,000 

Biological Technician Field data collection, assistance with 

analysis and report writing 0.3 $22,750 

Information and 

Education Specialist 

Assist in the development, design, and 

coordination of the step-down wildlife 

observation plan and develop and assist 

with the guided tour program 

0.3 $23,400 

Law Enforcement Officer Law enforcement 0.3 $20,800 

Park Ranger Facilities maintenance; take reservations 

for and assist in conducting guided tours 0.4 $15,600 

TOTAL FTES AND 

COSTS FOR STAFFING 2.9 $227,750
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 4 of 10 

Facilities 

Material/Facility 

Required 

Explanation of Need Cost 

Step-down Plan Needed to develop construction plans and 

specifications for observation areas and to describe 

and provide cost estimates for necessary amenities 

(i.e. benches, signage, fencing, viewing scopes, etc.) 

$35,000 

Observation Areas (with 

benches/fencing, scopes) 

Level sites with surfaces prepared to meet 

accessibility standards; amenities to aid in observing 

wildlife 

$70,000 

Regulatory signage and 

fencing 

Signs and appropriate fencing are required to 

delineate areas open to public access and those that 

are closed 

$30,000 

8 – 10 passenger van An accessible van with good visibility needed to 

accommodate seasonal guide tours $45,000 

TOTAL COST FOR 

FACILITIES $180,000 

The current Refuge budget is not adequate to fund all of the wildlife observation proposals 

included in the CCP, therefore, additional funding must be identified before these proposals 

can be implemented. It is possible to implement these proposals in phases as funding sources 

are identified. Potential sources for funding include Federal cost share grants, interagency 

partnerships, state and private grants, and contributions from Friends groups. 

Increasing the number of guided tours conducted on the salt works could be facilitated 

through the Refuge’s current partnership with the City of Chula Vista’s Nature Center. 

Additional funding, estimated at approximately $45,000, would be needed to acquire an 

additional van for the Refuge Complex and another $35,000 would be required to prepare the 

step-down wildlife observation plan and specific construction plans. The actual cost of 

developing the observation areas cannot be determined until more specific plans are 

development. 

Anticipated Impacts of the Use:

A number of studies have been conducted to evaluate the effects of wildlife observation and 

photography on wildlife. The studies are summarized in a literature review prepared for the 

Stillwater National Wildlife Refuge (DeLong and Schmidt 2000). In summarizing the 

findings of these studies, DeLong and Schmidt state that wildlife observation and 

photography can “negatively impact wildlife by altering wildlife behavior, reproduction, 

distribution, and habitat.” In addition, these studies show that birds frequently approached 

by humans may reduce foraging times in the area or avoid the area entirely. Huffman (1999) 

in observing waterbird disturbance in South San Diego Bay documented disturbance to 

migratory birds as a result of pedestrian activity along the shoreline. This disturbance was 

greatest during low tides when pedestrians left designated accessways to explore the 

mudflats. This activity affected both shorebirds and waterfowl. Huffman observed that 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 5 of 10 

human activity along the shoreline and in the mudflats would flush all birds within a 50 to 

100 meter radius. 

To reduce the potential for disturbance to wildlife, the majority of the new opportunities for 

wildlife observation and wildlife photography on the South San Diego Bay Unit would be 

provided along the perimeter of the Refuge rather than dispersed throughout the Refuge. For 

a discussion of the potential impacts to Refuge resources associated with wildlife observation 

and photography uses conducted in bay from water vessels, refer to the Compatibility 

Determination for recreational boating on the South San Diego Bay Unit. 

Endangered and Threatened Species: Human activity can have adverse impacts on 

endangered and threatened species, particularly when it disrupts bird nesting or foraging 

activities. Requests from the public to consider opening the levees around Ponds 10 and 

11(refer to Figure 2-6 of the Final CCP/EIS) to public access were evaluated in the CCP/EIS, 

where it was determined that such access could result in disturbances to nesting tern colonies 

located across the river channel (refer to the discussion of Nesting Season Disturbance 

below), as well as disturbances to an established California brown pelican (Pelecanus 

occidentalis californicus) roosting area located on the levee separating Ponds 10 and 11. 

Opening these levees to public access could also adversely affect the Federally-listed 

endangered light-footed clapper rail (Rallus longirostris levipes), which has been observed 

within the South Bay Biological Study Area, located immediately to the north of Pond 11. 

Potential threats to clapper rails from human activity on these levees consist primarily of 

direct habitat or nest losses resulting from human intrusion in the adjacent salt marsh areas. 

The effects of such disturbance would become even more significant following the 

restoration of Ponds 10 and 11, which are proposed for restoration to support the clapper rail. 

 Repeated intrusion into clapper rail occupied salt marsh habitat could disrupt foraging and 

intrusion into restored habitat could discourage the use of restored areas by this species. 

No adverse effects to listed species are anticipated from the current proposals to provide 

wildlife observation points around the perimeter of the Refuge. In addition, closing the salt 

works to guided tours during the nesting season would avoid any potential impacts to the 

Federally-listed endangered California least tern (Sternula antillarum) or threatened western 

snowy plover (Charadrius alexandrinus nivosus). 

Nesting Season Disturbance: The nesting season varies for each species, but can generally 

be described as occurring between mid-February and mid-September of a given year. 

Disturbance to nesting bird species may occur if persons are present in the vicinity of avian 

nesting colonies or individual nests. A variety of ground nesting avian species utilize the 

levees around the salt ponds for nesting, including colonies of Caspian terns (Sterna caspia), 

elegant terns (Thalasseus elegans), royal terns (Thalasseus maximus), gull-billed terns 

(Gelochelidon nilotica vanrossemi), Forster’s terns (Sterna forsteri), endangered California 

least terns and black skimmers (Rynchops niger). Loud noises from activities on adjacent 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 6 of 10 

areas could result in disturbances to those nesting colonies located closest to activity areas. 

Avian responses to disturbance can include flocking, alarm calling, nest abandonment, 

colony abandonment, and inter-colony antagonistic behaviors leading to crushed eggs and 

killed chicks. Predatory species, particularly avian predators such as northern harriers, 

ravens, crows, and other gulls, may also use disturbance episodes to depredate eggs and 

chicks while the adults are flocking or otherwise distracted by the initial source of the 

disturbance. 

The observation areas to be located along the southern edge of the Refuge would be situated 

approximately 150 meters or more from known nesting sites and physically separated from 

these sensitive areas by the Otay River channel. As a result, activities occurring at the 

observation areas would not be expected to result in disturbance to nesting seabirds. 

No guided tours of the salt works would be conducted during the nesting season; therefore, 

no nesting season disturbance from this use would occur. 

Sensitive Habitats: Although the proposed wildlife observation sites would be located 

around the perimeter of the Refuge, they would still occur in proximity to sensitive wetland 

habitat. Therefore, to avoid disturbance related impacts to sensitive habitat, such as 

trampling of vegetation, observation areas would be located along existing public trails 

and/or in areas where topographic relief or existing or future fencing would make it difficult 

for the public to gain access to sensitive areas. 

The potential for impacts to sensitive habitats as a result of guided tours would be negligible 

due to the level of supervision that would occur during such tours. 

Migratory Birds: Proposed observation areas have been sited away from locations that 

support an abundance of migratory bird foraging and loafing, therefore, disturbance from 

human activity in the vicinity of these areas is expected to be minimal. 

Disturbance and possible displacement of migratory shorebirds could occur around the salt 

works if guided tours result in excessive out-of-vehicle activity. According to DeLong and 

Schmidt (2000), Klein (1993) tested the behavioral response of waterbirds to human 

disturbance, including vehicular travel at Ding Darling NWR and found that as the intensity 

of disturbance increased, avoidance response by waterbirds tended to increase. Out-ofvehicle activity was also observed to be more disruptive than vehicular movement through 

the area. Although the degree of disturbance may vary for the species and local populations 

of waterbirds occurring within the South San Diego Bay Unit, similar differences between 

out-of-vehicle activity and vehicle travel related to guide tours through the salt works would 

be expected. 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

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Public Review and Comment:

Wildlife observation and photography have been discussed a several occasions at public 

workshops held in conjunction with the Comprehensive Conservation Plan (CCP) process. 

To initiate the CCP process, a Notice of Intent was published in the Federal Register on June 

23, 2000 (65 FR 39172). At that time, written comments were solicited. In July 2000, two 

initial scoping meetings were held, one in Imperial Beach and one in Chula Vista, to receive 

input from the public on issues related to the South San Diego Bay and Sweetwater Marsh 

Units. Due to the public’s level of interest in these refuges, focused public workshops were 

held in September 2000 and June 2001 to specifically address the issue of public use. Three 

additional workshops were held between November 2000 and May 2001 to receive input 

from the public on wildlife management and restoration proposals for these refuges. All of 

the public meetings were well attended with at least 40 people present at each meeting. 

Approximately 50 to 60 people attended those meetings related to public use. 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. One of these updates was devoted entirely to the topic of 

public use. These Planning Updates have been distributed to more than 1,000 individuals 

and organizations representing interested members of the public, conservation organizations, 

hunting, fishing and boating organizations, public agencies, municipalities, special districts, 

Tribes, and adjoining property owners. We received more than 50 letters, emails, and phone 

calls related to public use between June and November 2001 and numerous other 

communications relevant to public uses on the Refuge were received in 2002 and 2003. 

During the CCP scoping meetings and public use workshops, a number of individuals 

expressed their desire to see the needs of the Refuge’s wildlife met before any consideration 

is given to the provision of public uses on the Refuge. Others stated that the Refuge should 

be managed as a place for people as well as wildlife. With respect to wildlife observation, 

one individual requested that the ability to observe the sounds of wildlife on the Refuge, 

particularly during seabird nesting season, be preserved. The San Diego Audubon Society 

expressed an interest in having one or more viewing platforms provided near the salt works 

to permit viewing into the salt works. A number of potential observation areas were 

suggested, including those described above. 

The draft Compatibility Determination for wildlife observation and photography on the 

South San Diego Bay Unit was circulated for public review and comment as part of the San 

Diego Bay National Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental 

Impact Statement (CCP/EIS). Specifically, it was included in Appendix K of the draft 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 8 of 10 

CCP/EIS. The Notice of Availability for the draft CCP/EIS was published in the Federal 

Register on July 22, 2005 and a Planning Update announcing the availability of the Draft was 

sent to over 1,000 individuals, agencies, non-governmental organizations, and other 

stakeholders. In addition, the draft CCP/EIS was provided to over 275 interested parties and 

made available for review on the Refuge’s CCP website. Public comments were accepted 

through September 19, 2005. No comments related to this Compatibility Determination were 

received during the public comment period. 

 

Determination:

 Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations Necessary to Ensure Compatibility:

1. Prior to constructing any observation areas within the Refuge, a step-down wildlife 

observation plan that includes specific designs for the various observation areas will 

be developed and approved by the Refuge Manager. During the development of this 

plan, concepts will be reviewed with the adjacent community to receive comments 

and recommendations regarding its design. 

2. To reduce the potential for off-trail activity on Refuge lands and waters, regulatory 

signage and fencing or other appropriate barriers will be installed prior to opening an 

observation area. 

3. For three years following the completion of an observation area, monitoring shall be 

conducted during the nesting season to determine the effects, if any, of increased 

human activity at the site on nearby nesting seabirds. Additionally, weekly 

monitoring during peak migration periods shall also be conducted to observe any 

effects to bird foraging and resting behavior as a result of increases in activity at the 

observation site. If adverse effects are observed, additional measures shall be 

implemented to reduce disturbance. 

4. Guided tours of the salt works shall not be conducted during the nesting season 

(February 15 through September 15). From February 1 to February 14 and 

September 16 to September 30 of each season, the Refuge Biologist shall confirm one 

day prior to a scheduled tour that no nesting or fledgling activity is occurring on or 

within 150 meters of the tour route. 

5. To avoid excess disturbance during migration, the Refuge Manager shall establish 

guidelines for when and how often visitors on a guided tour are permitted to exit the 

vehicle for observation purposes. 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 9 of 10 

Justification:

Expanding the opportunities for wildlife observation and photography on the South San 

Diego Bay Unit will enhance the public’s appreciation of the wildlife resources supported 

within this Refuge. Although adequate funding is not currently available to implement all of 

the proposals, implementation can be phased over several years. As new opportunities are 

provided, the public’s appreciation for the species and habitats found within the Refuge will 

increase, and in turn conditions will improve for ensuring the protection and management of 

the Refuge’s listed species and other wildlife. This outcome is consistent with the Refuge 

purposes of protecting, managing, and restoring habitats for Federally-listed endangered and 

threatened species and migratory birds and maintaining and enhancing the biological 

diversity of native plants and animals. A review of the environmental consequences of 

implementing these uses, as provided in the Final CCP/EIS (USFWS 2006), demonstrates 

that these uses would not materially interfere with or detract from the fulfillment of the 

National Wildlife Refuge System mission, provided the stipulations to ensure compatibility 

are followed. Further, wildlife observation and photography are two of the six priority public 

uses of the System, as defined by the Act. Therefore, implementation of these programs 

would contribute to the fulfillment of the Refuge System mission, and the achievement of the 

goals established for the Refuge, particularly the goal to provide opportunities for compatible 

wildlife-dependent recreational uses that foster public appreciation of the unique natural and 

cultural heritage of South San Diego Bay. 

Mandatory Re-Evaluation Date: 

 X Mandatory 15-year Re-Evaluation Date (for priority public uses) 

 Mandatory 10-year Re-Evaluation Date (for all uses other than priority public uses) 

NEPA Compliance for Refuge Use Decision: 

_ _Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited:

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance 

on Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater 

National Wildlife Refuge (Draft). 
 

Final Wildlife Observation and Photography CD – South San Diego Bay Unit 

Page 10 of 10 

Huffman, Kathy. 1999. San Diego South Bay Survey Report – Effects of Human Activity 

and Water Craft on Wintering Birds in the South San Diego Bay. 

Klein, M. L. 1993. Waterbird Behavioral Responses to Human Disturbances. Wildlife 

Society Bulletin 21:31-39. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ Project Leader 

Approval: ______________________________Date: _________ 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 1 of 11 

Compatibility Determination

-FINALUse: Environmental Education and Interpretation

Refuge Name: South San Diego Bay Unit of the San Diego Bay National Wildlife 

Refuge 

(San Diego County, Cities of Coronado, Chula Vista, Imperial Beach, 

National City, and San Diego, California) 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the San Diego National Wildlife Refuge are the Fish 

and Wildlife Act of 1956, as amended (16 U.S.C. 742a-742j, not including 742d-742l), and 

the Endangered Species Act of 1973, as amended (16 U.S.C. 1531-1543).

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge was established: 

“to protect, manage, and restore habitats for federally listed endangered and threatened 

species and migratory birds, and to maintain and enhance the biological diversity of 

native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species Act of 1973, as 

amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as amended); 

”...for the development, advancement, management, conservation, and protection of fish 

and wildlife resources...for the benefit of the United States Fish and Wildlife Service, in 

performing its activities and services. Such acceptance may be subject to the terms of 

any restrictive or affirmative covenant, or condition of servitude...” (Fish and Wildlife 

Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 2 of 11 

Descriptions of Use: 

Various community members identified the development of environmental education and 

interpretation programs for the South San Diego Bay Unit as a key element of the 

Comprehensive Conservation Plan (CCP) for this Refuge. As a result, existing 

environmental education and interpretation programs are proposed for expansion. 

Environmental education, particularly the Habitat Heroes program, would be expanded to 

focus on new partnerships with area elementary, middle school, high school, and community 

college districts. In addition, a variety of interpretive concepts are proposed in response to 

comments received during the public workshop process. Many of these concepts would be 

implemented in conjunction with expanded opportunities for wildlife observation. New and 

expanded environmental education and interpretation programs are intended to provide the 

community and visitors to the region with an opportunity to better understand the wildlife 

and habitats found within the Refuge, increase public awareness for the need to protect these 

resources, and experience through interpretation the traditional wildlife-dependent 

recreational uses of the National Wildlife Refuge System. 

Environmental Education: As described in the Public Use Program discussion in Section 

2.3.2.3 of the Final CCP/Environmental Impact Statement (EIS) for the South San Diego Bay 

Unit (USFWS 2006), continuation of the Refuge’s Habitat Heroes program would provide 

elementary through community college students with the opportunity to participate in an 

innovative program that incorporates the use of GIS technology, traditional and internetbased instruction, cross-age student mentoring, and habitat-based investigations for the 

purpose of developing an appreciation for the importance of the coastal wetlands protected 

within the Refuge. This program would continue to focus on two significant threats to the 

habitat quality of these coastal wetlands: invasive plant species and stormwater pollution. 

Working on an upland area along the southern perimeter of the Refuge in Imperial Beach, 

students will have the opportunity to map native and nonnative plants, remove invasive plant 

species, and cultivate and plant native plants. The continued implementation of the program, 

which involves partnering with elementary, secondary, and post secondary students and 

teachers, volunteer groups, trained environmental educators, the City of Imperial Beach, and 

interested individuals from the surrounding community, will require the identification of 

additional funding sources. 

A significant activity of “Habitat Heroes” will be the inclusion of students’ work on a 

national web site with links to other such education programs in which the Complex 

participates called, “Hands on the Land.” Hands on the Land is sponsored by numerous 

federal agencies including the U.S. Fish and Wildlife Service and is funded by Congress 

through the National Environmental Education and Training Foundation. 

Environmental Interpretation: The interpretive program proposed for the South San Diego 

Bay Unit, as described in the Public Use Program discussion in Section 2.3.2.4 of the Final 

CCP/EIS (USFWS 2006), would include several components. The first is a proposal to 

design a variety of interpretive elements that would provide the public with an overview of 

the many resources present on the Refuge, including coastal wetland and upland habitats, 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 3 of 11 

migratory birds, colonial nesting seabirds, and endangered and threatened species. These 

interpretive elements would be installed around the southern perimeter of the bay, where 

visual and other sensory access into the Refuge is readily available. The second component 

involves a proposal to interpret one of the traditional wildlife-dependent recreational uses of 

the National Wildlife Refuge System, hunting. 

 

Opportunities for interpreting the resources protected within the Refuge would be provided 

along the strip of upland terrace that defines the Refuge’s southern boundary, generally the 

area immediately to the north of the Bayshore Bikeway (refer to Figure 2-14 in the Final 

CCP/EIS). Interpretive sites are proposed to generally correspond to the proposed wildlife 

observation areas, described in the Compatibility Determination prepared for wildlife 

observation and photography. These interpretive sites would be developed at the following 

locations: 1) between the northern terminus of 13th Street and the northern terminus of 

Florida Street; 2) at the northern terminus of 10th Street, near the City of Imperial Beach’s 

Public Works facility; and 3) at the northern terminus of 8th Street. All of these locations are 

located within the City of Imperial Beach. An observation area would be collocated at the 

interpretive site proposed for the end 10th Street. The City of Imperial Beach proposes to 

construct a bike path connection from the adjacent community onto the Bayshore Bikeway at 

this location, to develop a parking lot just to the south of the Refuge boundary, and to assist 

in the development of the proposed observation and interpretive site. The specific design for 

the proposed interpretive sites would be developed as part of a step-down interpretive plan. 

All of the proposed sites would be accessible from the Bayshore Bikeway and several public 

streets in northern Imperial Beach. A parking area that serves users of the Bayshore 

Bikeway is available at the northern terminus of 13th Street and on-street parking is available 

along Florence Street, 8th Street, and Boulevard Avenue. The interpretative areas would be 

accessible during daylight hours. The interpretive theme for each of these sites, the types of 

interpretive elements to be installed, and the detailed cost estimates for each interpretive site 

would be developed as part of the step-down plan. Opportunities for additional interpretation 

at existing public use locations where interpretive elements such as kiosks, signs, remote 

video cameras and other cutting edge approaches to public interpretation could be provided 

would also be examined in this step-down plan. 

Several members of the public expressed a desire to see hunting recognized on this Refuge as 

one of the traditional wildlife-dependent recreational uses of the National Wildlife Refuge 

System. To address this suggestion, the interpretive program for the Refuge would include 

the seasonal interpretation of a waterfowl hunting program along the northern levee of the 

salt ponds. This interpretive program, which would be conducted approximately four times a 

year between November and January, would involve up to 12 participants per session and 

each session would take place during the hours of sunrise to 9:00 a.m. One or two temporary 

hunting blind would be installed along the northern levee and as part of the interpretive 

program waterfowl historically harvested in the south bay would be called in to simulate the 

traditional hunting method. A docent would be present to describe historic hunting activities 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 4 of 11 

within the south bay, answer questions about waterfowl hunting programs in general, and 

discuss various hunting opportunities throughout the National Wildlife Refuge System. 

Participants would be transported from an off refuge location in vans and reservations would 

be needed to participate. No fee would be required to participate in this program. 

The CCP also recommends the development of a coordinated interpretive program for San 

Diego Bay that would involve collaboration among all of the agencies surrounding the Bay 

including the Cities of Coronado, Imperial Beach, National City, Chula Vista, and San 

Diego, County of San Diego, U.S. Navy, and Port of San Diego. The Refuge is interested in 

working with these agencies to interpret bay habitats and refuge resources in a coordinated 

style so that a member of the public traveling along the Bayshore Bikeway will be able to 

experience different yet harmonious interpretive elements that serve to enhance an 

understanding of the bay ecosystem as a whole, while allowing for individual interpretation 

of various discrete characteristics of bay habitats, endangered species, watershed issues, and 

cultural and historic values. 

Availability of Resources: 

To implement and administer the environmental education and interpretation programs 

described, the following staffing and materials/facilities would be required: 

Staffing 

Position Involvement FTE Cost 

Project Leader//Deputy 

Project Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.3 $27,300 

Refuge Operations 

Specialist 

Periodic on-site oversight, monitoring of 

law enforcement activities 0.3 $26,000 

Wildlife Biologist Monitoring, reporting, review interpretive 

plan, and provide oversight of bio tech 0.3 $26,000 

Information and 

Education (I&E) 

Specialist 

Coordinate the development of curriculum 

for the environmental education program 

and assist in the design of the interpretive 

plan, build partnerships with other 

agencies and organizations, and outreach 

to schools 

0.3 $23,400 

Law Enforcement Officer Law enforcement 0.3 $20,800 

Park Ranger Facilities maintenance, participate in the 

educational and interpretation programs, 

and assist with interpretive programs 

0.3 $15,000 

Maintenance Worker Maintain interpretive areas and amenities 0.3 $12,870 

Biological Technician Field data collection, assistance with 

analysis and report writing 0.3 $15,170 

TOTAL FTES AND 

COSTS FOR STAFFING 2.8 $214,240
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 5 of 11 

Facilities 

Material/Facility 

Required 

Explanation of Need Cost 

Step-down Plan Needed to design and prepare specifications for the 

interpretive sites proposed at the northern terminus of 

8th, 10th, and 13th Streets and to identify the 

interpretive theme for each area, the types of 

interpretive elements to be provided, and fabrication 

and installation specifications for the interpretive 

elements. 

$45,000 

Construct an Interpretive 

Trail w/ associated 

upland restoration on 

Refuge land near the 

northern terminus of 10th

Street 

To interpret the importance of coastal uplands to the 

function and value of coastal wetlands on an upland 

area; would involve the removal of nonnative 

vegetation and the installation of native plants and the 

construction of an a pathway through the restored 

area with access from the Bayshore Bikeway 

$35,000 

Interpretive elements for 

the interpretive trail 

Fabricate and install 20 small interpretive plant signs 

and three larger interpretive panels $15,000 

Temporary hunting blind To accommodate the interpretation of hunting in the 

South Bay and throughout the NWRS $500 

Development of 

educational curriculum 

for a middle school 

program 

Curriculum for the elementary school program has 

been developed, but a middle school curriculum for 

the Habitat Heroes program is still needed. 

$5,000 

Materials/Instructors to 

Implement the Habitat 

Heroes Program 

Annual costs associated with implementing the 

program including instructors, miscellaneous 

materials, and native plants $25,000 

TOTAL COST FOR 

FACILITIES $125,500 

The current Refuge budget is not adequate to fund all of the environmental and interpretive 

programs proposed, therefore, additional funding must be identified before these proposals 

can be fully implemented. The first year of the Habitat Heroes program was funded through 

a challenge cost share grant. To fully implement this program, which would involve 

expanding the program to reach elementary, middle, and high school students would require 

funding of approximately $25,000 annually. Funding could come from a combination of 

sources including the Refuge operating budget, funds from individual schools involved in the 

program and one-time or on-going public and private grant funds awarded to the Refuge’s 

Friends Group. Additional assistance would be provided by volunteers and participating 

teachers and student mentors. 

Implementation of the interpretation proposals could be phased to coincide with the 

identification of appropriate funding sources. Potential sources for interpretive funding 

include Federal cost share grants, state grants that focus on education and/or the 

environment, local partnerships, private funding sources, and contributions from the 

Refuge’s Friends group. Funding for the hunting interpretive program could be provided by 

local hunting groups and/or state and national organizations interested in traditional hunting 

activities. 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 6 of 11 

Anticipated Impacts of the Use: 

As described in Section 4.2.2.3 of the Final CCP/EIS (USFWS 2006), potential impacts 

associated with the implementation of the proposed environmental education and 

interpretation programs could include disturbance to wildlife, destruction of native habitats, 

and intrusion onto sensitive refuge lands by members of the public. Such impacts would be 

minimized through appropriate program design, adequate Refuge oversight and supervision 

of educational activities, and ongoing coordination among partners. 

 

Endangered and Threatened Species: Human activity can have adverse impacts to 

endangered and threatened species, particularly when this activity disrupts nesting or 

foraging activities. Through adherence to the stipulations outlined below, the potential for 

adverse impacts to the endangered light-footed clapper rail (Rallus longirostris levipes) that 

could occur as a result of increased human activity in the vicinity of the northern terminus of 

8th Street and between Ponds 10 and 10A would be minimized. As part of the design of 

future interpretive areas, issues such as location, size, orientation, construction timing and 

access, as well as specific activities to be permitted and physical improvements to be 

completed, would be reviewed by the Refuge Biologist to ensure that there would be no 

direct, indirect, or cumulative impacts to clapper rails or their habitat. It may be necessary to 

construct physical barriers such as post and cable fencing between the interpretive element 

and the wetlands to reduce the potential for habitat damage. These types of measures would 

be incorporated into the design of the interpretive areas as part of the future step-down 

interpretive plan. 

The interpretive elements proposed along the Bayshore Bikeway would be topographically 

separated from the more sensitive habitat areas within the Refuge making access into these 

areas difficult. The combination of natural barriers and the installation of additional post and 

cable fencing and signage would minimize the potential for impacts to clapper rails and other 

sensitive coastal wetland species. No adverse effects to the Federally-listed endangered 

California least tern (Sternula antillarum), the endangered California brown pelican 

(Pelecanus occidentalis californicus), or the threatened western snowy plover (Charadrius 

alexandrinus nivosus) are anticipated as a result of the current environmental education and 

interpretation proposals. 

The hunting interpretive program would be confined to the salt works and would occur 

during the non-breeding season; therefore, no adverse effects to endangered or threatened 

species are anticipated. 

Sensitive Habitats: The Habitat Heroes program would utilize an isolated, degraded upland 

area located on Refuge land. This upland, which is separated from nearby wetlands to the 

north by the Bayshore Bikeway, is located adjacent to a remnant of a much larger historic 

marsh area that was filled many decades ago to accommodate urban development. The 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 7 of 11 

playground of the Bayside Elementary School abuts the marsh to the south. Although the 

marsh supports several native coastal salt marsh plant species, it also includes various exotic, 

invasive plants and currently provides little benefit to native wildlife. The educational use of 

the adjacent upland could result in some trampling of native marsh vegetation; however, such 

impacts would be minimized through adequate teacher participation and monitoring of 

student activity. The proximity of this degrade marsh land provides opportunities to increase 

the students’ understanding of the importance of protecting wetland and native upland areas 

and adjacent watersheds. These benefits would outweigh the limited impacts to wetland 

plants from occasionally trampling. 

Locating interpretive areas around the perimeter of the Refuge, taking advantage of 

topographic barriers to separate public uses from sensitive resources, and installing 

appropriate signage and fencing where required would minimize the potential for impacts to 

sensitive habitats as a result of increased human activity. Public access onto the salt works 

during the nesting season is not proposed, therefore, no impacts to sensitive tern nesting 

habitat are anticipated. 

Migratory Birds: The salt ponds and mudflats along the edges of the Otay River support a 

diverse array of migratory birds including shorebirds, ducks, and seabirds. Various studies 

have shown that frequent human disturbance can negatively impact wildlife by altering 

wildlife behavior, reproduction, distribution, and habitat. Such disturbances may also cause 

birds to reduce their foraging times in these areas or avoid the areas entirely (DeLong and 

Schmidt 2000). Human activity in the vicinity of the proposed interpretive areas, particularly 

the areas to be located at the end of 10th Street and 8th Street, could result in some 

disturbance to resting and foraging migratory birds. These areas are already impacted to 

some degree by existing activities occurring along the Bayshore Bikeway. The addition of 

interpretive areas along the bikeway would likely increase the intensity of use resulting in an 

increase in the frequency of disturbance. Because the proposed interpretive elements and the 

environmental education program site are located along the perimeter of the Refuge, the 

birds that are flushed would likely move further into the Refuge and resume foraging or 

resting. Therefore, the effects of these uses on migratory birds are expected to be minimal. 

Disturbance and possible displacement of migratory shorebirds could occur around the salt 

works if guided tours result in excessive out-of-vehicle activity. According to DeLong and 

Schmidt (2000), Klein (1993) tested the behavioral response of waterbirds to human 

disturbance, including vehicular travel at Ding Darling NWR and found that as the intensity 

of disturbance increased, avoidance response by waterbirds tended to increase. Out-ofvehicle activity was also observed to be more disruptive than vehicular movement through 

the area. Although the degree of disturbance may vary for the species and local populations 

of waterbirds occurring within the South San Diego Bay Unit, similar differences between 

out-of-vehicle activity and vehicle travel could occur at the salt works. To avoid excessive 

disturbance, guides would reduce the number of stops in areas where high concentrations of 

foraging birds are located in proximity to the access road. 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 8 of 11 

Because the activity associated with the hunting interpretive program would be confined to 

one or two areas along the northern levees of Ponds 12, 14, and 15, disturbance along the 

mudflats would also be limited. In addition, this activity would be scheduled to occur during 

period of high tide when shorebirds are less likely to be present in large numbers. Based on 

the timing of the activity, which would coincide with the high tide, the small size of the 

groups, and the limited number of times that participants in this activity would be present 

along the levee during the year, disturbance impacts as a result of this activity would be 

minimal. 

 

Public Review and Comment:

Environmental education and interpretation have been discussed on several occasions at 

public workshops held in conjunction with the Comprehensive Conservation Plan (CCP) 

process. To initiate the CCP process, a Notice of Intent was published in the Federal 

Register on June 23, 2000 (65 FR 39172). At that time, written comments were solicited. In 

July 2000, two initial scoping meetings were held, one in Imperial Beach and one in Chula 

Vista, to receive input from the public on issues related to the Sweetwater Marsh and South 

San Diego Bay Units. Due to the public’s level of interest in these refuges, focused public 

workshops were held in September 2000 and June 2001 to specifically address the issue of 

public use. Three additional workshops were held between November 2000 and May 2001 

to receive input from the public on wildlife management and restoration proposals for these 

refuges. All of the public meetings were well attended with at least 40 people present at each 

meeting. Approximately 50 to 60 people attended those meetings related to public use. 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. One of these updates was devoted entirely to the topic of 

public use. These Planning Updates have been distributed to more than 1,000 individuals 

and organizations representing interested members of the public, conservation organizations, 

hunting, fishing and boating organizations, public agencies, municipalities, special districts, 

Tribes, and adjoining property owners. We received more than 50 letters, emails, and phone 

calls related to public use between June and November 2001 and numerous other 

communications relevant to public uses on the Refuge were received in 2002 and 2003. 

Opportunities for environmental education and interpretation were addressed at the initial 

scoping meetings for the CCP, as well as at the June 21, 2001 Public Use Workshop. Several 

members of the public expressed the desire to see the Refuge used as a setting for 

environmental education and others suggested the development of an interpretive area in 

proximity to the Bayside Elementary School. Creating partnerships with other agencies, 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 9 of 11 

school districts, and the adjacent community to implement educational programs was also 

emphasized. 

The draft Compatibility Determination for environmental education and interpretation on the 

South San Diego Bay Unit was circulated for public review and comment as part of the San 

Diego Bay National Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental 

Impact Statement (CCP/EIS). Specifically, it was included in Appendix K of the Draft 

CCP/EIS. The Notice of Availability for the Draft CCP/EIS was published in the Federal 

Register on July 22, 2005 and a Planning Update announcing the availability of the Draft was 

sent to over 1,000 individuals, agencies, non-governmental organizations, and other 

stakeholders. In addition, the Draft CCP/EIS was provided to over 275 interested parties and 

made available for review on the Refuge’s CCP website. Public comments were accepted 

through September 19, 2005. No comments related to this Compatibility Determination were 

received during the public comment period. 

Determination: 

 Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations Necessary to Ensure Compatibility: 

1. Each year, prior to initiating the Habitat Heroes program, all participating teachers, 

outside instructors, and other facilitators shall coordinate with the Refuge Manager to 

review the area-specific guidelines for implementing the program in a manner that 

will minimize impacts to wildlife and its habitat. These guidelines will specify the 

maximum number of participants per visit to the site, appropriate access routes into 

and through the site, the activities that can be conducted, and any times during the 

year when activities should be suspended or minimized. 

2. The Refuge’s Information and Education Specialist shall review all materials and 

programs to ensure consistency with Refuge goals and the mission of the National 

Wildlife Refuge System. 

3. All required regulatory signage and fencing or other appropriate barriers shall be 

installed prior to the opening of interpretive sites at the northern terminus of 10th

Street and 8th Street to reduce the potential for off-trail activity on Refuge lands and 

waters. 

4. Hunting interpretation programs will be scheduled to coincide with the high tide to 

reduce disturbance to migratory birds. 

5. Monitoring of the effects of increased human activity on migratory birds and nesting 

seabirds shall be implemented weekly during the first three years of the 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 10 of 11 

environmental education program and the first three years following the completion 

of an interpretive area. This monitoring should be conducted during peak migration 

periods, as well as during the nesting season, to determine what, if any, effect 

increases in activity as a result of these programs are having on bird foraging, resting, 

and/or nesting behavior. If excessive disturbance is observed, additional measures 

should be implemented to reduce these effects. 

Justification: 

The development of environmental education and interpretation programs for the South San 

Diego Bay Unit would provide various opportunities to inform community members and 

visitors to the region of the importance of the resources protected within the Refuge. In 

addition, the Habitat Heroes program is designed to encourage stewardship of the many 

resources protected in the Refuge. Although adequate funding is not currently available to 

implement all of the elements proposed within these programs, the phasing of program 

implementation over several years would have no adverse effects. Rather, the benefits of 

these programs would simply take longer to be realized. 

An informed and involved public, cultivated as a result of these programs, will benefit the 

wildlife and habitats protected and managed within the Refuge consistent with the Refuge 

purposes of protecting, managing, and restoring habitats for federally-listed endangered and 

threatened species and migratory birds and maintaining and enhancing the biological 

diversity of native plants and animals. A review of the environmental consequences of 

implementing these uses, as provided in the Final CCP/EIS (USFWS 2006), demonstrates 

that these uses would not materially interfere with or detract from the fulfillment of the 

National Wildlife Refuge System mission, provided the stipulations to ensure compatibility 

are followed. Further, environmental education and interpretation are two of the six priority 

public uses of the System, as defined by the National Wildlife Refuge System Improvement 

Act of 1997. Therefore, implementation of these programs would contribute to the 

fulfillment of the Refuge System mission, as well as the achievement of the goals established 

for the South San Diego Bay Unit, particularly the goal to provide opportunities for 

compatible wildlife-dependent recreational uses that foster public appreciation of the unique 

natural heritage of South San Diego Bay. 

Mandatory Re-Evaluation Date: 

 X Mandatory 15-year Re-Evaluation Date (for priority public uses) 

 Mandatory 10-year Re-Evaluation Date (for all uses other than priority public uses) 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 
Final Environmental Education and Interpretation CD – South San Diego Bay Unit 

Page 11 of 11 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited: 

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance 

on Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater 

National Wildlife Refuge (Draft).

U.S. Fish and Wildlife Service. 2006. Final San Diego Bay National Wildlife Refuge 

Comprehensive Conservation Plan/Environmental Impact Statement.

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Mosquito Management CD – South San Diego Bay Unit 

Page 1 of 10 

Compatibility Determination

-FINALUse: Mosquito Management

Refuge Name: South San Diego Bay Unit of the San Diego Bay National Wildlife Refuge 

(San Diego County, Cities of Coronado, Chula Vista, Imperial Beach, 

National City, and San Diego, California) 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the San Diego National Wildlife Refuge are the Fish 

and Wildlife Act of 1956, as amended (16 U.S.C. 742a-742j, not including 742d-742l) and 

the Endangered Species Act of 1973, as amended (16 U.S.C. 1531-1543). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge was established: 

“to protect, manage, and restore habitats for federally listed endangered and 

threatened species and migratory birds, and to maintain and enhance the biological 

diversity of native plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species 

Act of 1973, as amended) and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as 

amended); 

”...for the development, advancement, management, conservation, and protection of 

fish and wildlife resources...for the benefit of the United States Fish and Wildlife 

Service, in performing its activities and services. Such acceptance may be subject to 

the terms of any restrictive or affirmative covenant, or condition of servitude...” (Fish 

and Wildlife Act of 1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and 

regulations for the conservation, maintenance, and management of wildlife, resources 

thereof, and its habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System 

Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Mosquito Management CD – South San Diego Bay Unit 

Page 2 of 10 

Description of Use:

Mosquito management throughout the coastal refuges of San Diego County is conducted 

under the auspices of a Refuge Special Use Permit (SUP) in coordination with the San Diego 

County Department of Environmental Health, Vector Control Division. The SUP is issued 

annually. The primary purpose for implementing mosquito management on this Refuge is to 

avoid threats to public or wildlife health from specific mosquito-borne diseases. Mosquito 

management is implemented on the South San Diego Bay Unit through a phased approach 

that emphasizes early detection and treatment, if warranted, with larvicides. The use of 

adulticides is to be reserved for addressing human health emergencies. 

 

Several mosquito species occur in and around the South San Diego Bay Unit that are capable 

of transmitting microbial organisms that cause human diseases such as malaria and 

encephalitis. The mosquitoes of major concern in California belong to the genera Culex, 

Ochlerotatus, and Anopheles. The species of greatest public health concern include Culex 

tarsalis, Culex pipiens, Culex quinquefasciatus and Anopheles hermsi. Of lesser importance 

are the salt marsh mosquitoes: Ochlerotatus squamiger and Ochlerotatus taeniorhynchus. 

Specific data regarding the species presence in the vicinity of the Refuge was collected in 

2003 at the Otay River and Hollister Street mosquito trap array by the County of San Diego, 

Department of Environmental Health, Vector Control Division. This data indicates that eight 

species of mosquito are commonly found in this area. These species include: 

Anopheles hermsi – This species, which is very commonly found in the Otay traps, is a 

highly competent vector of malaria, although this disease is not prevalent in this region. 

Culex erythrothorax – This species, which is the most common mosquito in San Diego, is 

typically considered a nuisance. It is commonly found in the Otay traps and occurs in 

densely vegetated freshwater marshes and heavily vegetated backwater zones. It is not 

considered to be a major disease carrier, although its ability to potentially harbor West Nile 

Virus (WNV) is currently unknown. 

Culex tarsalis – A highly competent vector mosquito, this species is quite common in the 

Otay traps. Viewed generally as a nuisance mosquito, this species can also be an effective 

carrier of disease. 

Culiseta incidens and Culiseta particeps – These two species are regularly captured in the 

Otay traps in small to moderate numbers. Neither species is considered to be a disease 

vector, but can be a biting nuisance. Their ability to harbor WNV is unknown. 

Ochlerotatus increpitus – Primarily a nuisance mosquito, this species, which bites during the 

day, is common in the Otay traps. Its ability to vector WNV is unknown. 
 

Final Mosquito Management CD – South San Diego Bay Unit 

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Ochlerotatus taeniorhynchus and Ochlerotatus squamiger – These mosquito species are 

prevalent in salt marsh habitat. Ochlerotatus taeniorhynchus is primarily a day-biting 

nuisance, and neither species is currently considered to be a disease carrier; however their 

ability to transmit WNV is unknown. 

Mosquito management on this Unit is addressed through an integrated pest management 

approach in which Refuge staff and County vector control officials coordinate efforts to 

manage the overall environmental health of adjacent communities while minimizing impacts 

to Refuge trust resources. Working together, the two agencies agree upon issues related to 

access, methods of operation, and timing of access, as well as to exchange information 

related to listed species occurrences, permitting, and relevant agency policy. 

The current procedures for implementing mosquito management on this Refuge involve an 

annual meeting between County and Refuge staff to coordinate necessary permitting and 

implementation planning required to conduct mosquito monitoring and control on the Refuge 

for the upcoming year. Issues such as access points and pathways to be used by County 

personnel, appropriate hours of operation, and requirements for field coordination are 

discussed, agreed upon, and incorporated into the SUP. As part of this coordination process, 

County vector control personnel are provided with data generated by the Refuge biologist on 

listed species and other trust resources. County personnel share relevant data related to 

mosquito and disease monitoring in the vicinity of the Refuge. In addition, periodic 

meetings are conducted in the field with County field staff and the Refuge biologist to further 

coordinate activities. These meetings are scheduled throughout the season when warranted 

to ensure protection of listed species and to avoid disturbance to nesting birds. 

Following the conditions included in the SUP, County vector control personnel conduct 

periodic mosquito larvae surveys in many discrete areas throughout the Refuge. Because the 

primary means of mosquito management is the use of larvicides, it is essential that larvae be 

observed prior to pupation so that they may be treated appropriately by the least 

environmentally damaging means. As a result, the frequency of larvae surveys increases 

throughout the mosquito breeding season. Currently, treatment areas are determined based 

on the season, the species and density of the mosquitoes detected, the proximity of the 

vectors to surrounding urban areas, and the life stage the mosquitoes are found in. Control of 

adult or pupal mosquitoes is not currently conducted on the Refuge. 

Public concern over human health issues related to mosquito-borne disease has intensified on 

the west coast with the advance of WNV across the United States. To better address 

mosquito management, a phased response strategy has been developed for implementation 

on refuges in the Pacific Region. This strategy encourages an integrated pest management 

approach that incorporates habitat and best management practices to reduce the need for and 

use of insecticides on refuges, while also ensuring that legitimate human, fish, and wildlife 

health concerns are addressed. To implement this phased response strategy, current 
 

Final Mosquito Management CD – South San Diego Bay Unit 

Page 4 of 10 

procedures for managing mosquitoes on this Refuge will be augmented to better identify 

thresholds for mosquito treatment and present specific responses to various conditions 

encountered in the field. Under this new program, if mosquito population monitoring and 

disease surveillance (implemented by County vector control personnel) indicate that human 

health thresholds are exceeded, the use of larvicides, pupicides, and/or adulticides may 

become necessary. In some cases, emergency actions may be required that are not addressed 

by this Compatibility Determination. 

 

Two larvicide compounds that could be used to manage mosquitoes on the Refuge include 

Bti (Bacillus thuringienensis israelensis) and Altosid (methoprene). These larvicides are 

intended to control mosquitoes in wetlands prior to their emergence as adults. Bti is used 

primarily to control early stage larvae and is available in liquid and granular formulations. 

Altosid is used on later stage mosquito larvae and is available in liquid, briquet and pellet 

formulations. Both compounds are highly specific to mosquito larvae. The use of Golden 

Bear 1111, which is effective at preventing adult mosquito emergence from wetlands but 

toxic to fish and other aquatic organisms, is not currently permitted for use on the Refuge. 

The potential for mosquito production during and following brackish and freshwater wetland 

restoration on the Refuge would be reduced by appropriate restoration design, as described in 

Section 2.3.2.3 of the Final San Diego Bay NWR Comprehensive Conservation Plan 

(CCP)/Environmental Impact Statement (EIS) (USFWS 2006). Specifically, deeper water 

channels (greater than 4 feet) would be included in the design to break up areas of dense 

emergent vegetation and provide access for aquatic predators that feed on mosquito larvae. 

These restored wetlands would also include appropriate surveillance access points to aid 

County vector control personnel in monitoring wetlands for potential mosquito production. 

Availability of Resources: 

To implement and administer mosquito management on the South San Diego Bay Unit, the 

following staffing and facilities are required: 

Staffing 

Position Involvement FTE Cost 

Project Leader/Deputy Project 

Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.3 $30,300 

Refuge Operations Specialist On-site oversight 0.3 $26,000 

Wildlife Biologist Monitoring, mosquito 

management plan prep., 

coordination/oversight of 

vector control activities, 

annual prep. of SUP 

0.3 $26,000 

TOTAL FTES AND COSTS 

FOR STAFFING 1.3 $130,000 

TOTAL COST FOR 

FACILITIES 

none $0 
 

Final Mosquito Management CD – South San Diego Bay Unit 

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Adequate staff positions and financial resources are currently available and committed to 

implement mosquito management on the South San Diego Bay Unit. 

Anticipated Impacts of the Use: 

The purpose of this section is to critically and objectively evaluate the potential direct, 

indirect and cumulative effects mosquito management could have on the Refuge’s 

endangered and threatened species and other fish and wildlife resources. The evaluation of 

direct impacts focuses primarily on existing and future freshwater wetlands and coastal salt 

marsh areas of the South San Diego Bay Unit, as these portions of the Refuge are or will be 

most prone to mosquito production. The potential for indirect impacts to the remainder of 

the Refuge, which consists of the open bay, salt pond levees, mudflats, and upland habitat, is 

also evaluated. 

Habitat and Wildlife Disturbance: Vegetation trampling resulting from mosquito monitoring 

and mosquito control, as well as the possible creation of channels to drain stagnant water 

areas, could adversely impact native vegetation and wildlife habitat. In addition, these 

activities could result in disturbances to the existing wildlife that utilizes this area. At 

present, the Otay River floodplain and the existing salt ponds on the Refuge support both 

native and non-native vegetation and wetland habitats of varying types. The most significant 

habitats supported within the Otay River floodplain include freshwater marsh and willow 

scrub habitat, which occurs along the eastern portions of the Otay River channel and the salt 

marsh areas located along the western end of the river channel. These wetland areas provide 

foraging, resting, and nesting habitat for a variety of birds, including migratory shorebirds, 

waterfowl, and songbirds, as well as various native mammals, reptiles, and amphibians. To 

minimize impacts related to disturbance, the Refuge biologist would coordinate with County 

vector control personnel at least annually to review appropriate conduct within sensitive 

habitat areas. Specific field implementation protocols for working in sensitive habitat areas 

would be included in the Refuge SUP. 

Although the upland portion of the Otay River floodplain currently supports non-native 

vegetation, this area does provide foraging habitat for a variety of raptor species including 

northern harriers (Circus cyaneus), white-tailed kites (Elanus leucurus), American kestrels 

(Falco sparverius) and red-tailed hawks (Buteo jamaicensis). Foraging and nesting 

opportunities for raptors should not be reduced by mosquito control activities. 

Endangered and Threatened Species: One of the purposes of the South San Diego Bay Unit 

is to conserve fish and wildlife that are listed as endangered or threatened. A number of 

listed species occur within the boundaries of this Refuge, including several that utilize the 

wetland areas within the Otay River floodplain. The Federal endangered California least 

tern (Sterna antillarum browni) forages within the Otay River channel during the spring and 

summer, while the Federal endangered light-footed clapper rail (Rallus longirostris levipes) 

and State endangered Belding’s savannah sparrow (Passerculus sandwichensis beldingi) 
 

Final Mosquito Management CD – South San Diego Bay Unit 

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utilize the wetland habitats along the river channel year round. The cordgrass stands and 

brackish marsh habitat growing along the river channel provide foraging, resting, and/or 

breeding habitat for both species. 

Potential impacts to the light-footed clapper rail and Belding’s savannah sparrow would 

consist primarily of direct habitat or nest losses through trampling of cordgrass or 

pickleweed where nests could occur, but would also include indirect adverse affects related 

to the disruption of foraging opportunities in both clapper rail and Belding’s savannah 

sparrow territories. The relatively limited time that vector control personnel would be 

present in these habitat areas, as well as the use of those controlled access points and 

pathways agreed upon between the County and Refuge personnel and described in the 

Refuge SUP would minimize the potential for adverse affects to these species as a result of 

mosquito management. 

Mosquito control in this area does require some access to sensitive wetland areas; however 

no mowing or ditching of wetland areas is authorized. The level of allowed activity, 

combined with its controlled management by Refuge biological staff would not likely result 

in direct, indirect, and cumulative impacts to the light-footed clapper rail. 

Nesting Season Disturbance: The nesting season varies with species but can generally be 

described as occurring between mid-February and mid-September. Disturbance to nesting 

bird species may occur if vector control personnel are present in the vicinity of avian nesting 

colonies or individual nests. 

Several species, many of which are rare, sensitive or state and/or Federally-listed occur 

within the South San Diego Bay Unit. As described above, the habitats present within the 

Otay River channel support light-footed clapper rail and Belding’s savannah sparrow nesting. 

 Cordgrass stands along the Otay River channel and the brackish marsh within the channel 

support clapper rail nesting, while high salt marsh vegetation, such as the pickleweed stands 

that occur in the intertidal habitats within the river channel, are known to support savannah 

sparrow nesting. No nesting survey monitoring reports for the savannah sparrow are 

available for this location, but it is probable that nesting attempts by the species do occur 

within the area being evaluated. To avoid impacts to nesting species within the lower 

portions of the Otay River channel, periodic meetings would be conducted in the field with 

County field staff and the Refuge biologist to coordinate activities and delineate sensitive 

nesting areas that should be avoided or entered within extreme caution. 

 

There is also a potential for direct and indirect impacts to breeding waterfowl such as 

gadwall (Anas strepera) and mallard (Anas platyrynchos), which have also been observed 

nesting in the Otay River channel, however these impacts are not likely to be significant due 

to the controlled and limited nature of the access into habitat areas by authorized personnel. 
 

Final Mosquito Management CD – South San Diego Bay Unit 

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A variety of ground nesting avian species utilize the levees around the salt ponds for nesting, 

including colonies of Caspian terns (Sterna caspia), elegant terns (Sterna elegans), royal 

terns (Sterna maxima), gull-billed terns (Sterna nilotica vanrossemi), Forster’s terns (Sterna 

forsteri), endangered California least terns, and black skimmers (Rynchops niger). Avian 

responses to disturbance can include flocking, alarm calling, nest abandonment, colony 

abandonment, and inter-colony antagonistic behaviors leading to crushed eggs and killed 

chicks. Predatory species, such as ravens, crows, certain gulls, and harriers, may also use 

disturbance episodes to depredate eggs and chicks while the adults are flocking or otherwise 

distracted by the initial source of the disturbance. However, it is not anticipated that there 

will be a need in the immediate future for access by vector control personnel to the salt pond 

nesting areas. Implementation of restoration plans for the salt works (refer to Section 2.3.2.4 

of the Final CCP/EIS) would however restore wetland habitats in these areas that would 

require monitoring. Therefore, additional procedures for monitoring would be incorporated 

into the Refuge SUP following restoration to ensure protection of nesting seabirds, eggs, and 

fledglings. 

Future Impacts: As described above, the Final CCP/EIS (USFWS 2006) includes a proposal 

to restore portions of the South San Diego Bay Unit to native vegetation. The intent of this 

restoration is to restore habitat for the variety of sensitive and endangered species that 

currently and historically occurred in this area. Following restoration, the field 

implementation protocols for mosquito management that are included in the Refuge SUP 

shall be adjusted annually to incorporate new landscape conditions as they develop. 

To minimize the potential for successful mosquito breeding in restored wetlands, primarily 

brackish to freshwater areas, conditions that favor the development of thick stands of aquatic 

freshwater wetland vegetation would be avoided. Designs for all future restored wetland 

areas would take into account vector control related issues as well as habitat development. 

For instance, deep water areas (greater than 4 feet in depth) such as channels through the 

marsh would be constructed and maintained to provide open areas between stands of 

vegetation. This would provide access for mosquito predators such as fish and aquatic 

insects. Open areas of water would also make it difficult for female mosquitoes to lay eggs 

and mosquito larvae to find cover from predation. 

Public Review and Comment: 

Two public scoping meetings and a series of public workshops to discuss habitat 

management, restoration, and public use were held in conjunction with the CCP process. To 

initiate the CCP process, a Notice of Intent was published in the Federal Register on June 23, 

2000 (65 FR 39172). At that time, written comments were solicited. In July 2000, two 

initial scoping meetings were held, one in Imperial Beach and one in Chula Vista, to receive 

input from the public on issues related to the South San Diego Bay and Sweetwater Marsh 

Units. Due to the public’s level of interest in these Refuges, focused public workshops were 

held in September 2000 and June 2001 to specifically address the issue of public use. Three 
 

Final Mosquito Management CD – South San Diego Bay Unit 

Page 8 of 10 

additional workshops were held between November 2000 and May 2001 to receive input 

from the public on wildlife management and restoration proposals for these refuges. All of 

the public meetings were well attended with at least 40 people present at each meeting. 

At each workshop, the public was encouraged to provide verbal comments or to send us 

written comments following the workshop. A CCP web page 

(www.sandiegorefuges.fws.gov) was established to provide the public with specific 

information regarding the topics addressed at the various workshops and to present 

information regarding when and where to provide comments. A number of Planning Updates 

have also been prepared to summarize the progress of the CCP and to discuss specific issues 

related to the planning process. These Planning Updates have been distributed to more than 

1,000 individuals and organizations representing interested members of the public, 

conservation organizations, hunting, fishing and boating organizations, public agencies, 

municipalities, special districts, Tribes, and adjoining property owners. We received more 

than 50 letters, emails, and phone calls related to the CCP between June and November 2001 

and numerous other communications relevant to public uses on the Refuge were received in 

2002 and 2003. No public comments related to mosquito management have been received to 

date. 

The draft Compatibility Determination for wildlife observation and photography on the 

South San Diego Bay Unit was circulated for public review and comment as part of the San 

Diego Bay National Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental 

Impact Statement (CCP/EIS). Specifically, it was included in Appendix K of the Draft 

CCP/EIS. The Notice of Availability for the draft CCP/EIS was published in the Federal 

Register on July 22, 2005 and a Planning Update announcing the availability of the draft was 

sent to over 1,000 individuals, agencies, non-governmental organizations, and other 

stakeholders. In addition, the draft CCP/EIS was provided to over 275 interested parties and 

made available for review on the Refuge’s CCP website. Public comments were accepted 

through September 19, 2005. No comments related to this Compatibility Determination were 

received during the public comment period. 

Determination: 

 __Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations: 

1. The County of San Diego, Department of Environmental Health, Vector Control 

Division shall operate on Refuge lands under the terms and conditions outlined in a 

USFWS Refuge Special Use Permit, which shall be reviewed annually. 
 

Final Mosquito Management CD – South San Diego Bay Unit 

Page 9 of 10 

2. Special Use Permit conditions shall stipulate that all control work will be carried out 

in conformance with pre-approved USFWS Pesticide Use Proposals, Section 7 

Endangered Species Act consultations, and existing and future USFWS policies on 

mosquito management. 

Justification: 

Mosquito management would be implemented on this Refuge in accordance with the 

guidance provided for the Pacific Region by the Regional Office in March 2003. This 

guidance for mosquito management incorporates a phased-response strategy developed to 

manage mosquitoes in a manner that is compatible with refuge purposes and uses the best 

available science while minimizing impacts to fish and wildlife, which is consistent with the 

mission of the National Wildlife Refuge System. Mosquito management proposed for this 

Refuge would also address legitimate human, fish, and wildlife health concerns. 

Implementing mosquito control in accordance with the stipulations presented above would 

therefore not materially interfere with the ability to achieve the wildlife management goals 

established for this Refuge. 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited: 

U.S. Fish and Wildlife Service. 1985. Light-footed Clapper Rail Recovery Plan. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation 

Plan/Environmental Impact Statement. 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 
 

Final Mosquito Management CD – South San Diego Bay Unit 

Page 10 of 10 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 1 of 9 

Compatibility Determination

-FINALUse: Regional Trail

Refuge Name: South San Diego Bay Unit of the San Diego Bay National Wildlife Refuge 

(San Diego County, Cities of Coronado, Chula Vista, Imperial Beach, 

National City, and San Diego, California) 

Establishing and Acquisition Authorities: 

The authorities for the establishment of the San Diego National Wildlife Refuge are the Fish and 

Wildlife Act of 1956, as amended (16 U.S.C. 742a-742j, not including 742d-742l) and the 

Endangered Species Act of 1973, as amended (16 U.S.C. 1531-1543). 

Refuge Purposes: 

The San Diego Bay National Wildlife Refuge was established: 

“to protect, manage, and restore habitats for federally listed endangered and threatened 

species and migratory birds, and to maintain and enhance the biological diversity of native 

plants and animals” 16 U.S.C. § 1531-1543 (Endangered Species Act of 1973, as amended) 

and 70 Stat. 1119 (Fish and Wildlife Act of 1956, as amended); 

 

”...for the development, advancement, management, conservation, and protection of fish and 

wildlife resources...for the benefit of the United States Fish and Wildlife Service, in 

performing its activities and services. Such acceptance may be subject to the terms of any 

restrictive or affirmative covenant, or condition of servitude...” (Fish and Wildlife Act of 

1956). 

[This refuge] “shall be administered by him [Secretary of the Interior] directly or in 

accordance with cooperative agreements...and in accordance with such rules and regulations 

for the conservation, maintenance, and management of wildlife, resources thereof, and its 

habitat thereon...” (Fish and Wildlife Coordination Act of 1934). 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System is “to administer a national network of 

lands and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit of 

present and future generations of Americans” (National Wildlife Refuge System Administration 

Act of 1966, as amended [16 U.S.C. 668dd-668ee]). 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 2 of 9 

Description of Use: 

At the eastern end of the South San Diego Bay Unit is the Otay River floodplain. This area is 

included within the approved planning boundary of the Otay Valley Regional Park (OVRP), a 

multi-jurisdictional planning effort by the County of San Diego and the cities of San Diego and 

Chula Vista. The planning boundary for the OVRP, which was approved prior to the 

establishment of the South San Diego Bay Unit, encompasses more than 8,000 acres, and 

extends about 13 miles inland from the southeastern edge of the salt ponds at the mouth of the 

Otay River, through the Otay River Valley, to the land surrounding both Lower and Upper Otay 

Lakes. A Concept Plan for the OVRP was approved by the participating agencies in May 2001 

(County of San Diego 2001). One of the components of the OVRP, as described in the Concept 

Plan, is a proposal to create a regional trail through the Otay River Valley. The trail would 

extend east/west through the river valley, from the eastern planning boundary to the Bayshore 

Bikeway located to the west of Interstate 5 (I-5). To implement this proposal, the County of San 

Diego and supporters of the OVRP have requested that the Refuge allow the western end of the 

trail to extend through the Refuge where it would then connect with the Bayshore Bikeway. 

This Compatibility Determination addresses the proposal to designate an alignment through the 

Refuge for the future construction of a portion of this regional trail. Although the exact 

alignment of the trail will be worked out with the various agencies involved in implementing the 

OVRP, the alignment presented in the Comprehensive Conservation Plan (CCP) extends west 

from the I-5 undercrossing, north of the river channel, then travel northwest along the eastern 

border of the South San Diego Bay Unit for approximately 2,000 feet. When constructed, the 

trail would connect to the proposed Bayshore Bikeway near the northeastern corner of the 

Refuge. The Concept Plan does not include any specifics regarding the recommended width, 

proposed surfacing materials, or permitted uses for the trail, as these specifications would be 

worked out during step-down planning. The local agencies participating in the development of 

the OVRP would be responsible for obtaining approval from the Refuge Manager prior to 

constructing the trail, funding and installing the trail in accordance with the requirements placed 

on the project by the Refuge, maintaining the trail and associated amenities such as fencing and 

signage, monitoring trail use, and patrolling the trail to ensure compliance with established trail 

regulations. 

Once constructed, the trail would support two wildlife dependent recreational uses: wildlife 

observation and environmental interpretation. 

Availability of Resources: 

Designation of an alignment for the Otay Valley Regional Trail would not result in the 

expenditure of any additional Refuge funds and trail construction and maintenance, as well as 

required fencing and regulatory signage, would be the responsibility of the local agencies 

participating in the OVRP. However, refuge resources would still be required to assist the local 

agencies in developing a trail design that meets the approval of the Refuge Manager, as well as 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 3 of 9 

to monitor the potential effects of trail use on Refuge wildlife and native habitat. Periodic patrol 

by Refuge law enforcement would also be required; however, enforcement is already required in 

this area due to its proximity to urban uses. The following staffing would be required: 

Staffing 

Position Involvement FTE Cost 

Project Leader/ Deputy 

Project Leader 

General oversight 0.2/0.2 $25,700/$22,000 

Refuge Manager Periodic on-site oversight 0.3 $27,300 

Refuge Operations 

Specialist 

On-site oversight 

0.3 $26,000 

Wildlife Biologist Monitoring, reporting, assist in the design 

and siting of the trail, provide some 

oversight of trail construction and longterm monitoring of refuge resources 

surrounding the trail, oversight of 

biological technicians 

0.3 $26,000 

Refuge Planner Assist in the design and siting of the trail, 

provide some oversight of trail 

construction 

0.2 $16,510 

Park Ranger Assist in trail monitoring, facilities 

maintenance 0.3 $13,000 

Law Enforcement Officer Law enforcement 0.3 $20,800 

TOTAL FTES AND 

COSTS FOR STAFFING 2.1 $177,310 

Refuge staffing is adequate to accommodate law enforcement, wildlife monitoring, and planning 

related to trail design and layout. No Refuge funds would be needed for trail construction or 

long-term trail maintenance. Adequate resources are available to allow for this use. 

Anticipated Impacts of the Use: 

The proposed alignment for the future regional trail, which would extend along the Refuge’s 

eastern border, has been designed to avoid fragmentation of habitat and minimize impacts to 

wildlife. However, the construction and use of the proposed trail does have the potential to 

adversely affect the diversity and abundance of wildlife and the quality of its habitat. These 

impacts may include: direct loss of native vegetation; displacement of native vegetation due to 

the introduction of invasive species, including noxious weeds; and disturbance and displacement 

of wildlife. In addition, trail construction and trail use can disturb and compact soils, causing 

changes in infiltration and runoff that can lead to increased erosion and siltation in adjacent 

waterways (DeLong and Schmidt 2000). Unauthorized off trail activities can also occur 

resulting in additional disturbance and compaction of soil, vegetation trampling, and wildlife 

disturbance. 

In reviewing studies related to the influence of recreational trails on bird communities, Delong 

and Schmidt (2000) report that several of these studies suggest that both the physical presence of 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 4 of 9 

a trail and human disturbance associated with the trail can affect bird abundance, species 

composition, and nest predation in the immediate vicinity of a trail. Many of these impacts can 

be minimized through proper trail planning that limits fragmentation of habitat, avoids sensitive 

habitat areas, and establishes clearly defined paths to reduce off trail activities. The anticipated 

impacts of accommodating the proposed OVRP Trail are presented in detail in Chapter 4 of the 

Final CCP/EIS (USFWS 2006) and summarized below. 

Endangered and Threatened Species: One of the purposes for the establishment of the South San 

Diego Bay Unit is to protect Federally-listed endangered or threatened species. With the 

exception of the Federal endangered light-footed clapper rail, the habitats that support the 

Refuge’s listed species do not occur in proximity to the proposed regional trail alignment. If 

however off trail activities increase following the construction of the trail, disturbance to other 

listed species such as the Federal endangered California least tern (Sternula antillarum) and 

State endangered Belding’s savannah sparrow (Passerculus sandwichensis beldingi) could occur. 

Human activity can have adverse impacts on endangered and threatened species, particularly 

when their nesting or foraging activities are disrupted. Human activity within the Otay River 

floodplain could increase as a result of the construction of the proposed regional trail potentially 

impacting several sensitive species, including the clapper rail, which has been observed in the 

habitats that extend along the Otay River channel within the Refuge boundary. Threats to lightfooted clapper rail from humans consist primarily of direct habitat or nest losses due to trampling 

of vegetation where nests occur. Belding’s savannah sparrow utilize the higher salt marsh 

habitat that occurs near the western end of the river channel, as well as along the edges of the 

river channel further upstream. Human disturbance in these areas as a result of off trail activity 

could disrupt foraging activities, as well as result in direct habitat or nest losses through 

trampling of pickleweed. These species are also vulnerable to injury or death if dogs are not 

confined to the designed trail. The potential for off trail activity can be reduced through 

appropriate fencing and signage along the trail and patrol of the trail to regulate the activities of 

trail users. 

Nesting Season Disturbance: The nesting season varies for each species, but can generally be 

described as occurring between mid-February and mid-September. Disturbance to nesting bird 

species may occur if persons or dogs are present in the vicinity of avian nesting colonies or 

individual nests. 

Several species, many of which are rare, sensitive or Federally and/or State listed, nest within the 

South San Diego Bay Unit. As described above, the habitats present within the Otay River 

channel support light-footed clapper rail and Belding’s savannah sparrow nesting. Cordgrass 

stands along the Otay River channel and the brackish marsh within the channel provide nesting 

habitat for clapper rails, while high salt marsh vegetation such as the pickleweed stands that 

occur in the intertidal habitats within the river channel are known to support savannah sparrow 
 

Final Regional Trail CD – South San Diego Bay Unit 

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nesting. Off trail activities by humans and dogs would most likely result in direct adverse 

impacts to both of these species. Similar impacts to breeding waterfowl, such as gadwall (Anas 

strepera) and mallard (Anas platyrynchos), which have been observed nesting in the Otay River 

channel, could occur. 

Sensitive Habitats: With the exception of the native vegetation occurring within the river 

channel, the general area proposed for the future construction of the regional trail is highly 

disturbed and dominated by non-native, weedy vegetation. Under these conditions, the impacts 

of trail construction and trail use on sensitive habitats would be minimal, although unauthorized 

off trail activity could result in impacts to native wetland vegetation. The CCP proposes to 

restore the upland portions of the Otay River floodplain to native upland habitat necessitating 

coordination between restoration planning and trail design to avoid future impacts to restored 

upland areas. The proposed trail alignment is located along the perimeter of the Refuge to 

minimize the effects of habitat fragmentation. Once native upland vegetation is restored, 

impacts to this sensitive habitat could occur as a result of unauthorized off trail activities. These 

impacts could be avoided through the implementation of appropriate measures such as fencing 

and signage to discourage off trail activities by humans and dogs. Migratory Birds: The 

alignment proposed for the regional trail is located in an area that does not currently support 

migratory bird foraging and loafing, therefore activities on the trail would not be expected to 

impact these resources. However, if off trail activities were to occur, disturbance to migratory 

birds could result. The use of appropriate fencing and signage along the trail is expected to 

reduce the potential for off trail activities. In addition, by providing a well-designed trail within 

this area to accommodate recreational users, some of the existing unauthorized access on the 

Refuge could be reduced, resulting in minor benefits to Refuge resources. 

Public Review and Comment: 

The OVRP Trail has been discussed on several occasions at public workshops held in 

conjunction with the CCP process. To initiate the CCP process, a Notice of Intent was published 

in the Federal Register on June 23, 2000 (65 FR 39172). At that time, written comments were 

solicited. In July 2000, two initial scoping meetings were held, one in Imperial Beach and one in 

Chula Vista, to receive input from the public on issues related to the South San Diego Bay and 

Sweetwater Marsh Units. Due to the public’s level of interest in these refuges, focused public 

workshops were held in September 2000 and June 2001 to specifically address the issue of 

public use. Three additional workshops were held between November 2000 and May 2001 to 

receive input from the public on wildlife management and restoration proposals for these 

refuges. All of the public meetings were well attended with at least 40 people present at each 

meeting. Approximately 50 to 60 people attended those meetings related to public use. 

At each workshop, the public was encouraged to provide verbal comments or to send us written 

comments following the workshop. A CCP web page (www.sandiegorefuges.fws.gov) was 

established to provide the public with specific information regarding the topics addressed at the 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 6 of 9 

various workshops and to present information regarding when and where to provide comments. 

A number of Planning Updates have also been prepared to summarize the progress of the CCP 

and to discuss specific issues related to the planning process. One of these updates was devoted 

entirely to the topic of public use. These Planning Updates have been distributed to more than 

1,000 individuals and organizations representing interested members of the public, conservation 

organizations, hunting, fishing and boating organizations, public agencies, municipalities, 

special districts, Tribes, and adjoining property owners. We received more than 50 letters, 

emails, and phone calls related to public use between June and November 2001and numerous 

other communications relevant to public uses on the Refuge were received in 2002 and 2003. 

The provision of trails on the Refuge generated relatively few comments during the public 

scoping process and at the Public Use Workshop held on June 21, 2001. Comments that were 

provided included a desire to see limited access provided to those areas of the Refuge in which 

such use would be compatible with and not result in impacts to the Refuge’s sensitive wildlife 

resources. There was also a suggestion that a seasonal walking trail be provided around Ponds 

10 and 11, while others requested that all public access be prohibited with the salt works. 

The draft Compatibility Determination for wildlife observation and photography on the South 

San Diego Bay Unit was circulated for public review and comment as part of the San Diego Bay 

National Wildlife Refuge Draft Comprehensive Conservation Plan/Environmental Impact 

Statement (CCP/EIS). Specifically, it was included in Appendix K of the draft CCP/EIS. The 

Notice of Availability for the draft CCP/EIS was published in the Federal Register on July 22, 

2005 and a Planning Update announcing the availability of the draft was sent to over 1,000 

individuals, agencies, non-governmental organizations, and other stakeholders. In addition, the 

draft CCP/EIS was provided to over 275 interested parties and made available for review on the 

Refuge’s CCP website. Public comments were accepted through September 19, 2005. No 

comments related to this Compatibility Determination were received during the public comment 

period. 

Determination: 

 Use is Not Compatible 

 X Use is Compatible with the Following Stipulations 

Stipulations Necessary to Ensure Compatibility: 

1. Prior to the design and construction of the trail, the entity responsible for implementing 

the OVRP Concept Plan or one of Park’s member agencies shall enter into an agreement 

and/or obtain a Special Use Permit from the Fish and Wildlife Service. This agreement 

or permit to allow the installation and use of the proposed trail must outline the 

responsibilities of each agency. This agreement/permit should specify that the entity 

responsible for the OVRP will: 1) work cooperatively with the Refuge Manager in the 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 7 of 9 

design and proposed alignment of the trail; 2) receive written approval for the final trail 

design from the Refuge Manager; 3) be responsible for complying with all CEQA/NEPA 

requirements, as well as obtaining all required local, state, and federal permits for the 

trail; 4) finance and implement all aspects of trail construction including any required 

environmental mitigation and monitoring requirements, fencing, signage, and 

revegetation; 5) maintain the trail in perpetuity; and 6) establish and maintain a volunteer 

trail patrol to assist the agencies in monitoring trail conditions, the activities of trail users, 

and wildlife responses to trail use by the public. If an adequate number of volunteers (as 

determined by the Refuge Manager) cannot be found, a paid patrol officer should be 

provided in perpetuity, or until the OVRP volunteer program is activated. 

2. The specific route for the trail and any materials developed to publicize the trail shall be 

coordinated with and receive written approval from the Refuge Manager. 

3. The OVRP is responsible for the development and installation of special signage at both 

points along the trail where the trail enters Refuge property. This signage, which is to be 

in place before the trail is opened to public access, must explain that the trail is entering a 

National Wildlife Refuge and describe the importance of staying on the trail. 

4. Appropriate fencing and regulatory signage, which must be paid for and installed by the 

OVRP before the trail opens, is to be provided along the trail as it passes through the 

Refuge. 

5. The trail surface must be approved by the Refuge Manager and should consist of native 

soil, decomposed granite, or a hardened surface. 

6. Equestrian uses will not be permitted on the portion of the trail that crosses the Refuge 

lands. 

7. Use of the trail between dusk and dawn will be prohibited and this regulation should be 

included on all appropriate trail signage. 

8. All stipulations must be in place prior to opening the trail for public use. 

Justification:

The extension of the proposed Otay Valley Regional Trail onto refuge lands, if permitted in 

accordance with the stipulations listed above, would not materially interfere with or detract from 

the purposes for which the South San Diego Bay Unit was established or the fulfillment of the 

National Wildlife Refuge System mission. This trail, although not regarded as a priority public 

use, would provide the public with additional opportunities to observe wildlife on Refuge lands, 

therefore contributing to the goal of providing safe wildlife dependent recreational activities on 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 8 of 9 

the Refuge. 

Mandatory Re-Evaluation Date: 

 Mandatory 15-year Re-Evaluation Date (for priority public uses) 

 X Mandatory 10-year Re-Evaluation Date (for all uses other than priority public uses) 

NEPA Compliance for Refuge Use Decision: 

 Categorical Exclusion without Environmental Action Statement 

 Categorical Exclusion and Environmental Action Statement 

 Environmental Assessment and Finding of No Significant Impact 

 X Environmental Impact Statement and Record of Decision 

References Cited:

DeLong, Anita and Janet Schmidt. 2000. Literature Review: Effects of Human Disturbance on 

Wildlife with Emphasis on Wildlife-Dependent Recreation Relevant to Stillwater National Wildlife 

Refuge (Draft). 

County of San Diego. 2001. Otay Valley Regional Park Concept Plan. Adopted by the County 

of San Diego Board of Supervisors, the Chula Vista City Council, and the San Diego City 

Council. 

U.S. Fish and Wildlife Service. 2006. San Diego Bay National Wildlife Refuge (Sweetwater 

Marsh and South San Diego Bay Units) Final Comprehensive Conservation Plan/Environmental 

Impact Statement. 

 

Refuge Determination: 

Prepared by: ______________________________Date: _________

Refuge Manager/ 

Project Leader 

Approval: ______________________________Date: _________ 
 

Final Regional Trail CD – South San Diego Bay Unit 

Page 9 of 9 

Concurrence:

Refuge Supervisor: ______________________________Date: _________ 

Assistant Manager, Refuges 

California/Nevada 

Operations Office: ______________________________Date: _________ 

Manager, California/Nevada 

Operations Office: ______________________________Date:_________ 
 

Appendix L 

Fire Management Plan for the San Diego 

NWR Complex 
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement L-1

Appendix L: Fire Management Plan 

Summary 

The Department of the Interior (DOI) fire management policy requires that all refuges with 

vegetation that can sustain fire must have a Fire Management Plan that details fire management 

guidelines for operational procedures and values to be protected and/or enhanced. The San Diego 

National Wildlife Refuge Complex has year-round fire-funded personnel that are stationed at the 

San Diego NWR. 

The Fire Management Plan (FMP) for the San Diego National Wildlife Refuge Complex provide 

guidelines for appropriate suppression and/or prescribed fire programs at the San Diego Bay, San 

Diego, Seal Beach, and Tijuana Slough National Wildlife Refuges. With respect to San Diego Bay 

NWR, the plan focuses on preparedness, wildland fire operations, prevention, and detection. 

Prescribed and wildlife fire use are not proposed as a strategy for achieving land management 

objectives on this Refuge. 

The Plan outlines the fire management objectives for the Complex, describes the Complex’s 

wildland fire management situation, and presents the Complex’s fire management strategies. 

Values considered in the Fire Management Plan include protection of Refuge resources and 

neighboring private properties, effects of burning on refuge habitats/biota, and firefighter safety. 

Refuge resources include properties, structures, cultural resources, trust species including 

endangered, threatened, and species of special concern, and their associated habitats. The Fire 

Management Plan will be reviewed periodically to ensure that the fire program is conducted in 

accordance and evolves with the U.S. Fish and Wildlife Service (USFWS) mission and the San 

Diego National Wildlife Refuge Complex goals and objectives. 

Copies of the Fire Management Plan are available for review at the San Diego National Wildlife 

Refuge Complex, 6010 Hidden Valley Road, Carlsbad, CA 92011 or by contacting Victoria 

Touchstone, Refuge Planner, at (760) 431-9440 extension 349. 
 

Appendix M 

Final Predator Management Plan 
───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 1

Final 

PREDATOR MANAGEMENT PLAN 

San Diego Bay National Wildlife Refuge 

(Sweetwater Marsh and South San Diego Bay Units) 

I. Overview 

Pursuant to its endangered species management responsibilities and in conjunction with other 

wildlife and habitat management activities, the U.S. Fish and Wildlife Service (Service) will 

implement, per available funding, predator management on the San Diego Bay National Wildlife 

Refuge (Refuge). Species to benefit from this action include the Federal endangered California 

least tern (Sternula antillarum) and light-footed clapper rail (Rallus longirostris levipes) and the 

threatened western snowy plover (Charadrius alexandrinus nivosis). Predator management is 

identified in the draft San Diego Bay National Wildlife Refuge (NWR) Comprehensive 

Conservation Plan (CCP)/Environmental Impact Statement (EIS) (USFWS 2005) as one of several 

actions to be implemented in support of the Refuge’s listed species. 

This predator management plan has been developed as a comprehensive wildlife damage control 

program that addresses a range of management actions from vegetation control and nesting 

habitat enhancement to non-lethal and lethal control. The most effective, selective, and humane 

techniques available to deter or remove individual predators or species that threaten nesting, 

breeding, or foraging least terns, snowy plovers, or clapper rails will be implemented. 

II. Purpose 

The San Diego Bay NWR was established to conserve Federal endangered and threatened species. 

The two Refuge Units share the common goal of “supporting the recovery and protection efforts 

for Federal endangered and threatened species, other species of concern, and their habitats.” The 

objectives of this predator management plan are intended to assist the Service in achieving this 

goal and meeting the purpose for which the Refuge was established. 

The implementation of this predator management plan is intended to increase the productivity of 

the Refuge’s federally-listed endangered and threatened seabird and shorebird species. 

Numerous incidents of predation on listed species by a variety of native and nonnative mammalian 

and avian predators are documented annually within the Refuge. The Refuge, along with most 

other habitat available to California least terns, western snowy plovers and light-footed clapper 

rails, represent some of the best remaining examples of coastal wetland habitats in southern 

California. As such, these remaining habitats act as magnets for the community of migratory and 

endemic wildlife that survive in the current landscape. Urbanization has led to increased numbers 

of many species of generalist, common predators. The potential impact of increased native and 

non-native predator densities on endangered species populations is a significant impediment to 

their recovery. 

Reducing the number of California least tern, light-footed clapper rail, and western snowy plover 

adults, chicks, and eggs lost to predation is an important strategy in achieving the management 

objective of recovering and maintaining stable populations of these listed species on the Refuge. 

Other species that could indirectly benefit from predator management include the Federal 

endangered California brown pelican (Pelecanus occidentalis californicus), which roost along the 

salt pond levees of the South San Diego Bay Unit, and the State listed endangered Belding’s 
Appendix M ────────────────────────────────────────────── 

2 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

savannah sparrow, which nests in the pickleweed-dominated salt marsh habitat of both the 

Sweetwater Marsh and South San Diego Bay Units. Several species identified by the Service as 

Birds of Conservation Concern (USFWS 2002), including the black skimmer (Rynchops niger), 

elegant tern (Sterna elegans), and western gull-billed tern (Sterna nilotica vanrossemi), will also 

derive some benefits from the implementation of this plan. 

The western gull-billed tern, however, is a special case in the context of this plan. Since the South 

San Diego Bay Unit was established in 1999, the gull-billed tern has benefited from various Refuge 

management activities including predator management and nest site enhancement. Due in part to 

these Refuge management actions, the breeding population of this species at the salt works has 

increased from an estimated 11 to 20 breeding pairs in 1999 (Patton 2001) to approximately 40 

pairs in 2004 (Patton pers. comm.). During this same period, the number of least tern and snowy 

plover chicks lost to gull-billed tern predation has also increased (Patton 2004). This interaction 

between the gull-billed tern and the listed species that nest at the salt works cannot easily be 

addressed because of the extremely small population size of the western gull-billed tern. Various 

programs within the Service, including the Division of Migratory Bird Management, Ecological 

Services, and the National Wildlife Refuge System, are currently working together to identify 

appropriate actions that when implemented will ensure the recovery and conservation of all three 

of these trust species (least terns, snowy plovers, and gull-billed terns) throughout their range.

Predator Management Plan Objectives: 

• Increase the productivity of California least tern and western snowy plover by reducing 

the loss of eggs and chicks to predation and reducing the number of adult birds of these 

species that are lost or driven away by predators; 

• Reduce the loss of adult and juvenile light-footed clapper rails and eggs due to predation; 

• Reduce the number of individual problem predators in localized areas within the Refuge 

(Problem predators are defined as individual predators that are exhibiting hunting 

behavior in listed species nesting areas or essential habitat areas or that have been 

identified as actually preying on a listed species.); 

• Eliminate disturbance to roosting California brown pelicans by non-native mammalian 

predators; and 

• Reduce disturbance and predation by mammalian predators within seabird nesting 

colonies on the South San Diego Bay Unit. 

III. Background and Description of Problem 

California’s coastal wetlands provide essential habitat for a variety of avian species, including the 

Federal endangered and threatened species and other species of concern supported on the Refuge. 

The decline in the population of many of these species has been attributed to habitat loss, the 

introduction of exotic species populations, water and air pollution, habitat degradation, and human 

disturbance. The California Coastal Commission (1987) estimates that as much as 90 percent of 

California’s original coastal wetlands have been lost to development. Additionally, the majority of 

California’s sandy beaches that historically provided expansive habitat areas for seabirds, such as 

the California least tern, and shorebirds, like the western snowy plover, are now extensively 

utilized for human recreation and/or have been modified to support beachfront housing and other 

coastal development. 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 3

 

Today, coastal migratory birds are faced with two converging problems that seriously reduce 

reproductive success: limited viable nesting habitat and the concentration of native and non-native 

predators in proximity to nesting areas. The direct conversion of habitat to urban development 

and indirect losses of habitat resulting from increased human activity have greatly reduced the 

availability of suitable nesting areas. With fewer viable sites available, nesting seabirds and 

shorebirds are concentrated on fewer and more geographically limited nesting areas than 

previously occurred under more natural landscape conditions. Predation potential under current 

conditions has increased as predator foraging activities have become more intensely focused on the 

same remnant areas of coastal habitat that have been set aside for the protection of nesting 

migratory birds. Additionally, urban development has created conditions that are advantageous to 

many native, generalist predators resulting in larger populations of some predator species than 

were present historically. An abundance of non-native predators, such as feral dogs and cats and 

Virginia opossums, are able to enter the Refuge from adjacent urban areas. Their presence 

negatively impacts the viability of remaining coastal habitats for supporting endangered species. 

Many populations of southern California coastal nesting bird species are declining and others are 

endangered or threatened with extinction. Without human intervention, it is likely that several of 

these species will not survive. Reproductive success is strongly influenced by food availability, 

quality of breeding habitat, and predation pressure. Controlling the numbers of predators in 

endangered and threatened species habitats is the main variable that humans can directly control 

in a localized context. Providing additional breeding areas (protected nesting sites) to give the 

protected species greater opportunity to successfully breed continues to be pursued by land 

management agencies, however, there are very limited opportunities for such efforts in Southern 

California’s dense urbanizing environment. Therefore, management to reduce the potential for 

significant losses of threatened and endangered species due to predation on nesting grounds or 

other crucial habitat areas is an essential wildlife conservation goal. 

 Various conservation plans have been or are being developed that outline conservation priorities 

for specific assemblages, guilds, and communities of birds. Among the population conservation 

issues for waterbirds, as addressed in the North American Waterbird Conservation Plan (Kushlan 

et al. 2002), and the priority conservation actions for shorebirds, as outlined in the Southern Pacific 

Shorebird Conservation Plan (Hickey et al. 2003), is the need for appropriate predator 

management in waterbird and shorebird nesting areas. 

The following are brief summaries of relevant information relating to species populations targeted 

for protection under this predator management plan. 

California Least Tern

The California least tern is a loosely colonial, ground nesting, migratory seabird that returns 

from tropical latitudes to breed in southern California. Least tern nest sites are largely 

unvegetated, flat, open areas consisting of light colored, sandy surfaces near water bodies 

supporting abundant small fish. This tern once nested on beaches throughout southern 

California, south through Baja California, Mexico, and north to the San Francisco Bay area, 

however, increasing urbanization and habitat loss has led to the decline of its population with 

the majority of the remaining nesting colonies confined to San Diego and Orange Counties. 

With the loss of traditional beach nesting sites, this species has been forced to find alternative, 

less traditional nesting colony sites including landfills and airports (Patton 2002). 

The Service published a rule, effective June 2, 1970, listing the California least tern as 

endangered under the Endangered Species Act of 1973, as amended (ESA). The California 
Appendix M ────────────────────────────────────────────── 

4 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

least tern is endangered throughout its range as a result of the loss and degradation of nesting 

and foraging habitat and disturbance of nesting birds. Recovery actions described in the 

California Least Tern Recovery Plan (USFWS 1985a) include preserving and managing 

existing nesting colonies and providing new nesting sites in protected areas, maintaining 

adequate foraging habitat for nesting colonies, and minimizing disturbance and mortality by 

preventing human disturbance and minimizing predation. 

Today, nest sites are largely fixed in their location and size, with two of seven San Diego Bay 

sites falling within Refuge management responsibility. Historically, least tern nesting success 

at the salt works within the South San Diego Bay Unit has been poor although little active 

predator management occurred on the property until the Refuge Unit was established in 1999. 

On the Sweetwater Marsh Unit, the nesting success on the D Street Fill nesting area has been 

seasonally variable, with site disturbance and predation being the primary factors in least tern 

breeding failure. 

The least tern is vulnerable to a long list of predators, some of which are very abundant in 

urban environments, such as feral or domestic cats and dogs, American crows (Corvus 

brachyrhychos), and American kestrels (Falco sparverius). In the 2000 nesting season, 20 

species were observed preying on or taking a least tern egg, chick, fledgling, or adult in 

California. Twelve of these species are considered possible predators on the Refuge (Patton 

2002); including feral dog, coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), 

opossum (Didelphis virginiana), peregrine falcon (Falco peregrinus), American kestrel, gullbilled tern, and various gull species. Between 1999 and 2002, there were numerous 

documented losses of California least tern chicks due to predation. 

Under this plan, the nest site management actions presented below will be implemented to 

improve least tern reproductive success. 

• Vegetation management to control weeds, avoid excessive plant growth, and maintain 

barren, sandy areas occurs annually at the D Street Fill in partnership with the 

Unified Port of San Diego (Port); 

• Nesting substrate is periodically enhanced by adding clean, light sand to various salt 

pond levees; 

• Signs and fencing are maintained in various areas to reduce human and mammalian 

disturbance in seabird nesting areas; 

• Endangered species monitoring has been conducted annually in the nesting colonies to 

record reproductive success and document factors affecting success including 

disturbance and predation (monitoring will continue in accordance with available 

funding); 

• Predator monitoring is conducted annually during the nesting season to provide 

current data regarding the presence of predators within the vicinity of the nesting 

colony and to document and address incidents of predation within the colony; 

• Active nest sites are often protected using tiles, exclosures, and other physical devices 

to reduce accessibility of eggs and chicks to predators; and 
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───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 5

• All mammalian predators observed in nesting areas are removed and individual 

problem avian predators may be controlled as appropriate to reduce loss of least tern 

eggs, chicks, and adults. 

Western Snowy Plover

On March 5, 1993, the Pacific coast population of the western snowy plover was listed as 

threatened under the provisions of the ESA. The western snowy plover is threatened 

throughout its range as a result of the loss and disturbance of habitat and nesting sites. There 

are only a handful of snowy plover breeding locations currently used in southern California. 

Regularly used locations include Bolsa Chica (Orange County), Camp Pendleton, Batiquitos 

Lagoon, Naval Amphibious Base-Coronado, Silver Strand State Beach, and Tijuana Estuary in 

San Diego County. Within the South San Diego Bay Unit, snowy plover nesting occurs 

regularly at the salt works (six of the last nine years) with one to four nest attempts each year. 

Unfortunately, reproductive success has been poor. No nest attempts were observed at the 

salt works in 2003. Between two and ten snowy plover nesting attempts with poor 

reproductive success have historically occurred at the D Street Fill on the Sweetwater Marsh 

Unit, however, since 2000, there have been no known nesting attempts by snowy plovers in this 

area. Disturbance and predation are the most likely reasons for this poor history of 

reproductive success. 

The list of potential predators of snowy plover eggs and chicks is long. During extensive 

surveys of breeding and wintering snowy plovers conducted in San Diego County between 1994 

and the winter of 1999, it was determined that most nest failures in 1994, 1996 and 1997 were 

the result of predation (Powell et al. 2002). Documented egg predators included corvids 

(ravens and crows), coyotes, Argentine ants and gulls. Although the causes of chick mortality 

are more difficult to determine, several species were determined to be likely causes of 

mortality during these surveys including great horned owl (Bubo virginianus), burrowing owl 

(Athene cunicularia), gull-billed tern, and American kestrel. Due to high densities in 

surrounding urban areas, corvids, kestrels, and feral dogs and cats represent significant 

threats to the snowy plover population on this Refuge. 

The Western Snowy Plover Pacific Coast Population draft Recovery Plan (USFWS 2001) 

includes the prevention of excessive predation of snowy plover as one of the recovery tasks 

requiring implementation to maximize the survival and productivity of this species. The draft 

plan encourages the employment of an integrated approach to predator management that 

considers a full range of management techniques and recommends seeking assistance from 

U.S. Department of Agriculture (Wildlife Services Branch) biologists, State wildlife agency 

biologists, and others. Specific management techniques addressed by the plan include manual 

removal of litter and garbage from nesting areas, removal of predator perches and unnatural 

habitats, use of predator exclosures where appropriate, removal of predators where warranted, 

and removal of bird and mammal carcasses in nesting areas. These actions, as well as those 

described for the California least tern, will be implemented on the Refuge under this plan. 

 

Light-footed Clapper Rail

Light-footed clapper rails are year-round residents of coastal salt marshes and lagoons, 

although they may also occasionally be found upstream in freshwater marsh habitat. 

Generally, they nest in the lower littoral zone of a salt marsh where dense stands of cordgrass 

(Spartina foliosa) are present (USFWS 1985b). As a result of the destruction of coastal 

wetlands throughout southern California, the total population of light-footed clapper rails 

became so seriously low that on October 13, 1970, this species was added to the Federal list of 

endangered species and was designated as endangered within the United States. 
Appendix M ────────────────────────────────────────────── 

6 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

The leading threats to clapper rails are salt marsh habitat loss, degradation, and 

fragmentation. These rails are also threatened by disturbance, diseases, contaminants, and 

predation. Potential predators of clapper rail eggs, nestlings, and adults include California 

ground squirrel (Spermophilus beecheyi), rats (Rattus spp.), long-tailed weasels (Mustela 

frenata), garter snakes (Thamnophis sp.), striped skunk (Mephitis mephitis), feral dogs and 

cats, opossum, and a variety of hawks and owls (USFWS 1985b). The Recovery Plan for the 

Light-Footed Clapper Rail (USFWS 1985b) includes as a recovery action the need to identify 

and control predators within marshes where predation is believed to be a significant problem. 

Clapper rails within the Refuge suffer from a lack of adequate high-tide refugia which limits 

the rails’ ability to hide when forced out of the salt marsh during high tide events. It is a goal 

the Refuge to restore and manage a fully functional coastal salt marsh/coastal sage scrub 

transitional habitat for the protection of the rail during its entire life cycle. However, this is a 

long-term commitment and will take many years to achieve. The rail will need additional 

management measures intended to protect and restore its populations including predator 

management. The FWS is currently working with several partner agencies to develop a 

captive breeding protocol development program for the light-footed clapper rail. This program 

seeks to bolster the genetic and demographic diversity of the species within isolated wetlands 

in the United States. As salt marshes are restored, it is hoped that various management 

actions taken now, will give the species the best possible chance to remain viable within coastal 

salt marshes in southern California well into the future. 

The following actions will be implemented to protect the Refuge’s clapper rail population: 

• Regulatory signage and periodic patrol by the Refuge law enforcement office is 

provided to minimize human disturbance in clapper rail habitat; 

• Nesting platforms are maintained in the marsh to provide chicks and eggs with 

enhanced protection from avian predators; and 

• Year-round predator monitoring is conducted to identify and control native and 

non-native mammalian predators that pose a threat to the rails. 

California Brown Pelican

The California brown pelican was listed as endangered on June 02, 1970 because of widespread 

pollutant-related reproductive failures. This bird is extremely sensitive to bioaccumulation of 

the pesticide DDT (and other organochlorine pesticides), which causes reproductive failure by 

altering calcium metabolism and thinning eggshells (USFWS 1983). Although California 

breeding populations have rebounded since the elimination of DDT use, the continued presence 

of DDT and its byproducts in the ecosystem, as well as other factors, still threaten this species. 

Delisted in1985 in the areas of the U.S. Atlantic coast, Florida, and Alabama, this species is still 

considered endangered within California, Louisiana, Mississippi, Oregon, Puerto Rico, Texas, 

Virgin Islands, Washington and Central and South America. 

 

Today, the availability of adequate food supplies is a major concern for the long-term recovery 

of this species. Commercial over-harvesting of Pacific mackerel, Pacific sardine, and the 

northern anchovy has resulted in less food availability for these birds, particularly during the 

breeding season. Pelicans are also threatened by human development along the coast, which 

increases disturbance to these birds in their breeding and resting habitats. The availability 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 7

and quality of roosting and loafing areas influence the energy budgets and reproductive 

potential of these birds (Jaques and Anderson 1987). Management of these essential habitats 

to minimize disturbance is therefore important for both breeding and non-breeding birds. The 

South San Diego Bay Unit, particularly the levee between Pond 10 and 11 within the salt 

works, is an important roosting area for brown pelicans during the non-breeding season. Feral 

and domestic dogs, coyotes and human disturbance represent the largest threats to these 

roosting pelicans. Roosting opportunities within the South San Diego Bay Unit were recently 

expanded to include a floating platform within the salt works. The use of this platform will be 

monitored and if adequate numbers of pelicans are using the platform for night roosting, 

additional platforms may be installed. 

Birds of Conservation Concern

The 1988 amendment to the Fish and Wildlife Conservation Act mandates the Service to 

“identify species, subspecies, and populations of all migratory non-game birds that, without 

additional conservation actions, are likely to become candidates for listing under the 

Endangered Species Act of 1973.” To meet this mandate, the Service has prepared Birds of 

Conservation Concern 2002 (USFWS 2002), which is intended to accurately identify the 

migratory and non-migratory bird species (beyond those already federally designated as 

threatened or endangered) that represent our highest conservation priorities and draw 

attention to species in need of conservation action. The goal of the Service is to preclude the 

need for additional bird listings under the Endangered Species Act by implementing proactive 

management and conservation actions. Within the Sweetwater Marsh Unit, four of the 

shorebirds that frequent the marsh have been identified as Birds of Conservation Concern; 

these include the whimbrel, long-billed curlew, marbled godwit, and short-billed dowitcher. Six 

shorebirds and three colonial nesting seabirds included on the list of Birds of Conservation 

Concern 2002 are supported by the habitats within the South San Diego Bay Unit. These 

species include the whimbrel, long-billed curlew, marbled godwit, black turnstone, red knot, 

short-billed dowitcher, gull-billed tern, elegant tern, and black skimmer. The elegant tern and 

black skimmer could indirectly benefit from the implementation of this predator management 

plan. 

Gull-Billed Tern (Gelochelidon nilotica vanrossemi) 

Management for the suite of avian species that utilize the Refuge is complex and difficult. 

The species conflicts inherent in managing the changing community of organisms utilizing 

coastal wetlands in southern California today present challenges that traditional wildlife 

managers may never have encountered historically. A case in point is the western gullbilled tern in San Diego Bay. 

The gull-billed tern is designated as a Bird of Conservation Concern (BCC) at the national, 

regional (USFWS Pacific Region), and local scale (Southern Coastal California Bird 

Conservation Region). The Fish and Wildlife Conservation Act (1988 Amendment) 

requires that the Service “identify species, subspecies, and populations of all migratory 

non-game birds that, without additional conservation actions, are likely to become 

candidates for listing under the Endangered Species Act of 1973". BCC 2002 is the 3rd

edition of this congressionally-mandated list and represents the most comprehensive effort 

thus far to identify species in need of active conservation measures. The gull-billed tern 

was included in the list because of its declining population trends and threats to breeding 

birds. At the subspecies level, the western gull-billed tern is of increased concern due to its 

extremely small population size (<600 known nesting pairs range-wide), limited 

distribution (ten sites range-wide), suspected population declines, and threats during the 

breeding season. The BCC designation does not impose regulatory conditions; however, 
Appendix M ────────────────────────────────────────────── 

8 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

birds included on the BCC 2002 list are deemed priorities for conservation actions. In 

addition, under Executive Order 13186, “Responsibilities of Federal Agencies to Protect 

Migratory Birds,” Federal agencies are to avoid and/or minimize adverse impacts on birds, 

and BCC species in particular, while conducting agency actions and are encouraged to 

restore and enhance habitat for migratory birds. Additionally, one of the Service’s primary 

goals is to conserve avian diversity in North America. Conserving ecosystem diversity is 

one of the goals of the National Wildlife Refuge System. 

The western gull-billed terns that nest at the salt works benefit from a number of recovery 

actions implemented to conserve the California least tern and western snowy plover. 

These recovery actions include habitat protection, habitat enhancement, reduced human 

disturbance, and predator management. In addition to the benefits of refuge management 

and management for endangered species recovery, the Service has also been monitoring 

the gull-billed terns at the salt works and throughout its range to better understand the 

population size, nesting ecology, and conservation needs of this species. In 2003, the 

Service joined with biologists in Mexico to conduct comprehensive surveys of gull-billed 

terns in western Mexico. The results of these surveys were reported in Palacios and 

Mellink (2003). 

 

Based on the information available to date, the estimated population of this subspecies in 

western Mexico is 376 breeding pairs, with 80 percent of the population occurring within 

two relatively large colonies (Cerro Prieto, Baja California and Laguna de Pericos, 

Nayarit) (Palacios and Mellink 2003). Within the United States, this subspecies only 

nests in two locations: the Salton Sea and the salt works within the South San Diego Bay 

Unit. The combined population of these two colonies in 2003 is estimated at about 190 

breeding pairs (Seto pers. comm.). Ongoing monitoring of gull-billed tern colonies by the 

Service and others will improve our understanding of the breeding biology and distribution 

of the gull-billed tern range-wide. Information provided by these studies will also assist in 

developing management actions to conserve this species. Further, we will be able to better 

assess how conservation of the gull-billed tern can be coordinated with ongoing 

endangered species recovery actions in Southern California. 

Gull-billed tern nesting on the South San Diego Bay Unit was first documented in 1987 

(Terp and Pavelka 1999). Between 1999 and 2004, the number of breeding pairs at the 

salt works has slowly increased from between 11 and 20 in 1999 (Patton 2001) to 

approximately 40 in 2004 (Patton pers. comm.). Unlike the other colonial nesting seabirds 

at the salt works, the gull-billed tern is an opportunistic feeder, foraging on a variety of 

terrestrial and aquatic animals. A recent study conducted in San Diego Bay by Molina and 

Marschalek (2003) found small invertebrates (primarily mole crabs, Emerita analoga) and 

small fish to be the primary prey items delivered by adults to chicks. Lizards (Uta

stansburiana and Sceloporus occidentalis), insects, and small black-necked stilt 

(Himantopus mexicanus), killdeer (Charadius vociferus), western snowy plover and 

California least tern chicks were also part of the gull-billed tern’s diet. The first report of 

gull-billed tern predation on a least tern chick occurred in 1988 in Mississippi (Densmore 

1990). Predation of least tern and western snowy plover chicks by gull-billed terns has 

been documented at the San Diego Bay NWR since 1999 (Patton pers. comm.). 

Over the past few nesting seasons, gull-billed terns nesting at the salt works have become 

effective predators of young least tern and western snowy plover chicks. The largest 

losses occurred in 2003, when 54 chicks were known to be lost to gull-billed tern predation. 

During the 2004 nesting season, 43 chicks were lost to gull-billed terns. It should be noted 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 9

that these are minimum numerical estimates of listed species chick losses due to the fact 

that observers are only present at certain times. Biologists monitoring these nesting 

populations infer that depredation by gull-billed terns on snowy plover and least tern 

chicks is ongoing when observers are not present, therefore, the impacts that gull-billed 

terns have had on the productivity of nesting sites throughout San Diego Bay and the 

Tijuana Estuary are not insignificant (Brian Collins pers. comm.). 

 

Since 2001, the Service has met with private biologists, land managers, and Service staff 

prior to each nesting season to discuss strategies for addressing gull-billed tern predation. 

Based on input from these meetings, the Service has chosen to refrain from conducting 

predator control actions on the gull-billed tern. The question of whether or not the Refuge 

should manage the size of the gull-billed tern colony at the salt works in an effort to reduce 

the loss of least tern and snowy plover chicks to gull-billed tern predation was raised again 

during the preparation of this predator management plan. Based on the desire to 

maintain/enhance the numbers of breeding gull-billed terns in Southern California, it was 

determined that no lethal control of this species will be considered at this time. Instead, 

over the next few years, the Service will implement several actions to address gull-billed 

tern predation of least terns and snowy plover chicks including the initiation of a pilot 

project to experiment with different types of chick shelters for California least terns and 

developing an experimental design to better document avian predation on both least terns 

and snowy plovers. In addition, during the 2005 breeding season a limited monitoring 

program of the gull-billed tern colony at the salt works will be implemented to evaluate 

nesting activity, reproductive success, and predation activities. The Service’s Migratory 

Birds Program will also continue to work with partners in Mexico to complete year two of a 

range-wide survey for gull-billed terns. 

 

IV. Existing Predator Management Efforts in the San Diego Bay Region 

San Diego National Wildlife Refuge Complex. The San Diego National Wildlife Refuge 

Complex (Complex) currently conducts a variety of management activities on the Tijuana Slough 

NWR, Sweetwater Marsh Unit, and South San Diego Bay Unit for the purpose of protecting 

colonies and/or pairs of California least tern, western snowy plover, light-footed clapper rail, and 

other Federal trust species of migratory birds. Management activities currently conducted to 

minimize attractants to predatory populations include: trash management, installation and 

maintenance of perimeter fencing in some locations, removal or trimming of large shrubs and trees 

in proximity to nesting areas to reduce the availability of resting and perching areas, and the use of 

various forms of exclosures over the nests of some species such as the western snowy plover. 

Another activity, public education and outreach, is an important component of the predator 

management program conducted at the Tijuana Slough NWR. This involves ongoing education 

programs relating to endangered species, the annual distribution of educational materials to the 

local community just prior to the nesting season. These materials address the problems associated 

with intended or unintended feeding of feral populations of domestic animals, clearly identify 

wildlife protected areas, and explain the importance of responsible control of household pets to the 

Refuge’s wildlife species. Special emphasis, usually in the form of door-to-door distribution of 

materials, is placed on getting these materials to those residents who live immediately adjacent to 

the Refuge. 

Predator management activities are closely coordinated with regular biological monitoring of 

nesting colonies in part to provide evidence of the identity of problem predators and the magnitude 

of the predation impacts to listed species populations. When indirect means do not provide 
Appendix M ────────────────────────────────────────────── 

10 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

adequate protection based upon data gathered through biological monitoring, direct predator 

management actions, including non-lethal and if necessary lethal control, are implemented. 

Unified Port of San Diego. The Unified Port of San Diego (Port) manages two sites surrounding 

the Bay, including tern nesting areas within Lindbergh Field (San Diego International Airport) 

and the Chula Vista Wildlife Reserve. The D Street Fill portion of the Sweetwater Marsh Unit is 

co-managed by the Port and the Service, which each owns a portion of this fill area. Management 

is similar to that conducted on the San Diego Bay NWR and includes site preparation, annual 

monitoring, and predator control. USDA APHIS-WS currently conducts active predator 

management on these areas under contract with the Port. 

United States Navy. The United States Navy manages three of the six current least tern and 

snowy plover nesting areas surrounding San Diego Bay. These three locations are located within 

the Naval Air Station North Island and Naval Amphibious Base Coronado. Management is similar 

to that conducted on the San Diego Bay NWR and includes site preparation, annual monitoring, 

and predator control. However, some nesting areas occur within heavily used training areas and 

the Navy’s training needs may influence the timeliness of these programs. The Navy has 

historically contracted with USDA APHIS-WS for predator management implementation at these 

sites. 

Interagency Coordination. Coordination among agencies is ongoing and statewide pre and postbreeding season least tern and western snowy plover meetings are held annually to discuss plans 

and results of the various management programs for that season. These meetings provide the 

opportunity to discuss what actions are most effective in achieving the recovery goals for the 

various endangered and threatened species covered by these programs. Additionally, interagency 

meetings are periodically scheduled to address species-specific issues related to predation and 

recovery. Interagency meetings to address issues related to gull-billed terns have been conducted 

since 2001. These meetings have led to support for continuing population assessments for the 

species, as well as support by some for the candidacy as threatened or endangered for the western 

North American population of the gull-billed tern. 

V. Management Plan 

The predator management plan for the San Diego Bay NWR will be implemented to reduce 

damage by predators to Federal threatened or endangered species populations. The threat may 

be to adults, chicks, or eggs. A range of management actions, including non-lethal and lethal 

control, will be implemented. As such, the plan represents a comprehensive wildlife damage 

control program that will integrate and apply practical methods of prevention and control to 

reduce damage by wildlife while minimizing the harmful effects of the control measures on 

humans, other species, and the environment. The activities conducted on the Refuge will vary 

depending upon the specific wildlife damage problem that is occurring. A particular predator 

problem may be addressed through the implementation of activities related to resource 

management, physical exclusion, wildlife management, or any combination of these. 

For most predatory species, removal will be accomplished primarily by hazing or live trapping and 

secondarily by lethal control. In all cases, the most humane methods available will be used. 

Efforts will be made to avoid and minimize losses of non-target native wildlife and all uninjured 

non-target species inadvertently captured will be immediately released near the site of capture or 

at a suitable location at the discretion of the Refuge Manager. 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 11

Direct control methods will include live-capture and translocation of individual predators; the 

intentional hazing (scaring off) of predatory species from nesting areas; and in some cases the 

lethal removal of problem predators. Lethal removal, which may involve shooting or the use of 

body grips or gas cartridges, may be used to remove predators that are identified as known and 

immediate threats to endangered or threatened species within the Refuge. Only licensed and 

authorized agencies or individuals will implement predator management actions. 

 

Without continued management of mammalian and avian predators, the Refuge’s population of 

light-footed clapper rails could be eliminated and the population size and nesting success of snowy 

plovers and least terns could decline dramatically. As a result, the Service believes that the 

following approach to predator management within the various areas of the Refuge will achieve the 

goals, objectives, and legal mandates of the Service on the San Diego Bay NWR. 

D Street Fill

This 40-acre area on the Sweetwater Marsh Unit will continue to be jointly managed by the 

Service and the Port. Management will include the removal of weedy vegetation and control of 

shrubs and other potential perching or hiding areas for avian and mammalian predators. To 

reduce accessibility to the site by large mammals, the Service will continue to maintain the 

fence and gate at the eastern edge of the property. Roof tiles, exclosures, and other nest 

shelters will also be used when deemed appropriate to minimize take of eggs and chicks by 

avian predators. Under this plan, predator monitoring on the D Street Fill will be conducted 

during the nesting season. Endangered species monitoring within the nesting colony will also 

be conducted provided that adequate funding is available. Throughout the nesting season 

(March through September), the colony will be monitored for signs of specific predators, 

tracks, or other indicators of the presence of mammalian predators in the vicinity of nesting 

areas. The area will also be monitored for evidence of losses due to avian predators. 

Endangered species monitoring of nesting colonies will provide hatch and fledge rates, as well 

as adult survivorship and population size. 

The predators that will be most commonly targeted for control include feral cats and dogs, 

California ground squirrels, Virginia opossums, Norway and black rats, striped skunks, 

common raven, American crow, and western gull. Prior to each nesting season ground 

squirrels will be lethally removed from the site to reduce the loss of tern and plover eggs. 

Coyotes, foxes, and other native mammalian predators will be trapped or shot when found 

within the nesting colony. 

Non-lethal methods will be emphasized as the preferred tool for controlling avian predators. 

During the nesting season only, individual problem avian predators may be live-captured and 

later released in a suitable location. In cases where trapping is unsuccessful and an individual 

predator has learned to depredate tern or plover eggs and chicks, the predator may be lethally 

removed upon approval of the Refuge Manager. 

Salt Pond Levees

Management actions to protect nesting least terns and western snowy plovers on the salt pond 

levees of the South San Diego Bay Unit will be similar to those described for the D Street Fill. 

Levee tops and other nesting areas will be maintained annually as needed. Fencing will be 

installed as needed to reduce access into the area by mammals, and predator monitoring will 

occur during the nesting season. During monitoring, dead animals that might attract 

predators to the area will be removed from the site. 

 
Appendix M ────────────────────────────────────────────── 

12 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

Paradise Marsh/Sweetwater Marsh/Otay River Floodplain

Predator management will also be implemented within those areas of the Refuge that support 

the endangered light-footed clapper rail. The clapper rail is a year-round resident of the 

Refuge; therefore, predator management will also be conducted year-round. Various actions 

will be taken to reduce clapper rail predation. A public outreach program will be conducted 

annually to inform nearby residents of the adverse effects that cats and dogs can have on the 

species. Unauthorized access by the public into sensitive marsh areas will be controlled 

through signs, fencing, and patrol by law enforcement personnel. Nesting platforms will be 

installed and maintained where appropriate to protect eggs and young clapper rail chicks. 

Mammalian predators are the primary predators of concern for this species. These include 

domestic and feral cats, raccoons, and the non-native red fox, among others. Predator 

monitoring will be implemented throughout the year to look for signs of specific predators, 

tracks, or other indicators of the presence of mammalian predators in the marsh that could 

pose a threat to the rails. Avian predators are documented to take light-footed clapper rails. 

Avian predators will be treated on a case-by-case basis. Non-lethal methods will be tried first 

before implementing lethal removal. 

VI. Direct Control of Predators - Species Specific Protocols 

The direct control of predators on the Refuge has historically been implemented by U.S. 

Department of Agriculture (USDA), Animal and Plant Health Inspection Service, Wildlife Services 

(APHIS – WS) through an interagency agreement with the Service. It is likely that this 

arrangement will continue in the future, provided funds are available. Contracts will be issued 

annually and will include detailed descriptions of approved control methods, disposition procedures 

for captured predators, and species-specific protocols. Predator management will be implemented 

year-round, although the majority of the contracted activities will occur during the breeding 

season. During the non-breeding season for endangered species, APHIS – WS will concentrate on 

the control of feral dogs and cats and mammalian predators such as skunks and opossums, which 

pose a threat to the light-footed clapper rail. 

Various types of equipment and techniques will be used to implement predator management on the 

Refuge and all such implementation will occur in accordance with federal and state regulations. 

The preferred control methods include live trapping and hazing. Knowledge of the particular 

predator’s habits, particularly the habits of avian predators, will determine which trapping 

technique is employed. 

Live trapping may include the use of box type mammal traps, Bal-chatri traps [a type of baited 

monofilament line leg-hold/cage trap], scent baited padded leg-hold traps and perch pole traps. 

Manual capture methods may also be employed using hand held capture poles or other manual 

techniques. Traps are inspected in accordance with State Fish and Game Code and Service policy. 

Specifically, traps set out overnight for mammalian predators are checked within two hours of 

sunrise and traps left out during daylight hours are monitored regularly and checked a minimum 

of four times per day. Traps set for avian predators may be left out overnight if nocturnal 

predation is considered a threat to protected species. The use and monitoring of pole traps will be 

conducted in accordance with Service policy. 

Hazing may be used to deter particular predators at the discretion of the Refuge Manager, and can 

include the use of firearms, pyrotechnics, and/or audio or visual stimuli. 

When deemed necessary, lethal removal by shooting, body grip traps, and gas cartridges may be 

used to take predators that are identified as known and immediate threats to endangered or 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 13

threatened species. Lethal removal of avian predators is most often employed when an individual 

problem predator has focused its foraging activities on the nesting colony. In this case, an entire 

colony’s productivity or even survival can be jeopardized in a short time frame. One such example 

occurred in 1997. A pair of burrowing owls was observed preying on adult and chick California 

least terns at the Tijuana Estuary. Refuge staff determined that live trapping was the preferred 

method of control because of a concern for the sensitivity of the local burrowing owl population. 

Over about a 12-day period (the time it took to locate and live-capture the owls), this pair of owls 

had taken between 70 and 80 breeding adult least terns and an unknown number of chicks. This 

one event resulted in the lost of approximately 18% of all breeding individuals in the colony during 

that nesting season (Patton 1998). Under this plan, selective removal of individual problem 

predators will be permitted for all avian predators with the exception of gull-billed terns. 

Routine predator monitoring will be conducted in the nesting colonies. Problem predators may be 

identified through direct observation of predators in the act of hunting or preying on listed species. 

The presence of predators in the colony can also be established through the identification of tracks 

of birds, reptiles, or mammals in the nesting colony, dissection of raptor pellets (disgorged 

undigested material from previous meals), observations of preyed-upon individuals, eggs, or other 

material. In many cases these observations can be used to identify, at least to species, the predator 

impacting the site. 

Some problem predators will defeat all attempts at hazing or live trapping and will be removed by 

lethal methods. Prior approval from the Refuge Manager is required for all actions involving the 

lethal removal of a predator. This approval for lethal removal may be in the form of blanket 

discretionary removal of certain species found within the confines of the breeding colony site (such 

as for corvids, feral dogs, or feral cats where live trapping has been ineffective and nesting has 

begun) or on a case-by-case basis (such as for identified individual raptors). 

Although not approved for use on these Refuges at this time, the avicide DRC 1339, a pesticide 

used to control corvid populations, may be approved for use in the future if deemed necessary, to 

control corvids. DRC 1339 is injected into chicken eggs, which are then secured onto strategically 

placed elevated bait stations in the vicinity of endangered species nesting areas. Ingestion of the 

pesticide is lethal to the crow or raven. Specific baiting and pre-baiting activities are conducted to 

eliminate the possibility of attracting non-target species. 

Species Specific Protocols

Procedures for intervention with predators will be dependent upon several factors, including, 

but not limited to: 1) the degree of threat the individual predator poses to protected 

populations; 2) the native or non-native status of the predator; 3) the conservation status of 

specific predator species populations; and 4) the general condition of a particular protected 

species nesting colony including; species, nest colony phenology, relative disturbance levels 

from other sources, numbers of vulnerable individuals on site, and other factors. 

The following species may be trapped or otherwise removed if observations, tracks, or other 

indicators of the presence of the species are found within the vicinity of protected species’ 

nesting areas during the nesting season, or if it is determined that the species poses a threat to 

light-footed clapper rails or roosting California brown pelicans: domestic and feral dogs and 

cats, coyote, red fox, gray fox, California ground squirrel, Virginia opossum, striped skunk, 

raccoon, Norway rat, black rat, common crow, common raven, or injured gulls. 

The following native avian species will be live trapped from the immediate vicinity of nesting 

terns and plovers, when they are determined to pose a threat to these species by USDA 
Appendix M ────────────────────────────────────────────── 

14 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

APHIS-WS in consultation with the Refuge Manager: American kestrel, loggerhead shrike, 

barn owl, great horned owl, burrowing owl, red-tailed hawk, sharp-shinned hawk, Cooper’s 

hawk, and various gull species. 

The following species require prior consultation with the Refuge Manager before lethal or nonlethal control actions can be taken: peregrine falcon, northern harrier, and short-eared owl. 

 

Disposition of Captured Animals

All raptors and other avian predators that are live captured will be removed and held in a 

licensed/permitted rehabilitation/holding center until they can be released back into the wild. 

Release will be at a suitable location after the endangered species nesting season is completed. 

Holding facilities and the location of all release sites must be approved by the Refuge 

Manager. 

All non-native mammalian predators, other than dogs and cats, will be euthanized using 

approved humane methods. Target and non-target predators that are injured during trapping 

will be treated on a case-by-case basis. These animals may be euthanized or taken to an 

approved rehabilitation/veterinary care facility depending on species and extent of injuries. 

All non-target wildlife (animals determined not to be a threat to protected species) that is 

captured unharmed will be immediately released near the capture site or at another suitable 

location. All domestic or feral dogs and cats, when feasible, will be taken to an approved 

shelter facility operated by a cooperating local unit of government, humane society or a 

veterinary care facility. 

VI. Monitoring and Reporting 

Implementation of this predator management plan will be monitored and a report will be issued 

annually describing the actions taken to control predation and the numbers and types of predators 

controlled. In addition, the report will include documented incidents of predation on listed species, 

recommendations on how predation might be further reduced, and an evaluation of how the 

current year’s predator management actions relate to the objectives established for this plan. 

VII. Cooperators 

This plan will be implemented in cooperation with the following agencies and organizations, as 

appropriate: 

• Fish and Wildlife Service, Carlsbad Ecological Services Field Office 

• Fish and Wildlife Service, Division of Migratory Birds and Habitat Programs, Region 1 

• California Department of Fish and Game 

• U.S. Department of Agriculture, Animal Plant Health Inspection Service -Wildlife Services 

• Unified Port of San Diego 

• San Diego County Department of Animal Control 

• Project Wildlife 

VIII. Other Recovery Actions to be Implemented on the Refuge 

Predator management is just one of several strategies that will be implemented to achieve the 

management goal of recovering and maintaining stable populations of the Federal threatened and 

endangered species and species of concern that occur within the Refuge. Other strategies 

described in detail in the San Diego Bay NWR Comprehensive Conservation Plan (CCP) include 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 15

expanded habitat and wildlife management activities, habitat enhancement, and habitat restoration 

strategies are described below. 

Various management strategies are proposed in the CCP to minimize human disturbance of 

sensitive habitat areas, including fencing, signage, and public education and outreach. Habitat 

enhancement is proposed to improve tidal circulation within existing marsh habitat, improve the 

quality of the nesting substrate for ground nesting birds, and expand the availability of cordgrassdominated salt marsh habitat to support the clapper rail. 

 

The CCP also includes a variety of habitat restoration proposals that would provide additional 

nesting, foraging, and resting habitat for endangered and threatened species and other species of 

conservation concern. Within the Sweetwater Marsh Unit, coastal salt marsh restoration is 

proposed that would provide additional nesting and foraging habitat for the light-footed clapper 

rail and additional habitat for foraging least terns and a variety of migratory shorebirds. Large 

areas of coastal salt marsh restoration are proposed within the South San Diego Bay Unit that 

would benefit the clapper rail, least tern, and various Birds of Conservation Concern. Also 

proposed is the creation of additional nesting areas that could benefit the least tern and snowy 

plover, as well as several colonial nesting seabirds. Water management proposals within the salt 

ponds could also provide additional nesting and foraging habitat for the western snowy plover. 

IX. Alternatives Considered 

In addition to the predator management plan presented above, various alternative methods for 

addressing predation of listed species on the Refuge were considered. These included: 

• Non-lethal Control Only 

• Indirect Control Only (implement management activities that reduce predation without 

non-lethal or lethal removal of predators) 

• No Predator Management

Proposed Plan

The proposed predator management plan combines direct actions to control predation along 

with indirect actions related to reduced disturbance and improved habitat quality. The Service 

believes this proposal represents the most effective and most humane alternative. 

Non-lethal Control Only 

A predator plan that relies on the control of all predators using only non-lethal methods could 

have devastating effects on the Refuge’s least tern and snowy plover populations. This is 

particularly true if an avian predator learns to prey on the eggs or young of a listed species. In 

some cases, considerable time can pass before a problem predator is trapped; as was the case 

in 1997 involving a pair of burrowing owls at the Tijuana Slough NWR (refer to Section IV.). 

Because lethal removal was not implemented in this case, the offending burrowing owls took a 

large number of chicks and more importantly, breeding adults. These events had a lasting 

effect on productivity at the site since losses of breeding adults can have population effects for 

many seasons. Least terns can be quite long-lived birds and may make many nesting attempts 

in their lives. 

Indirect Control Only

Indirect control of predation would involve implementing management activities that reduce 

predation without lethal or non-lethal removal of predators. Instead, measures such as the use 

of visual and auditory repellents and physical barriers would be employed. Visual and auditory 

repellants are limited by several factors, including: 1) unintentional hazing of protected 
Appendix M ────────────────────────────────────────────── 

16 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

species while attempting to haze predatory species; 2) reduced effectiveness over time as some 

predatory species become accustomed to particular stimuli and begin to ignore them; 3) 

difficulties in effectively deploying such repellents in the field; and 4) limited effectiveness of 

repellents on particular species. Physical barriers are a part of an integrated predator 

management program and will be used for some purposes such as keeping most off-leash dogs 

out of the nesting colonies. However, physical barriers in the absence of the ability to remove a 

predator are ineffective in controlling avian predation, as well as some forms of mammalian 

predation. The use of exclosures over nesting plovers has been effective in protecting eggs, 

but once the chicks leave the exclosure, they are once again vulnerable to predation. Although 

predation reduced to some extent through indirect control, this reduction in loss is not 

considered adequate to achieve the goals and objectives of the Refuge for listed species. 

No Predator Management

Under this alternative, no actions would be taken on the Refuge for the specific purpose of 

controlling predators. Mammalian and avian predators would not be harassed or specifically 

deterred from traveling or flying through the Refuge or entering the nesting colonies. Based 

on previously documented losses of listed species to predation, it is likely that the Refuge’s 

population of least terns, snowy plovers, and light-footed clapper rails would no longer be able 

to achieve sustainability goals for fledging success. In addition, a dramatic reduction in nest 

productivity could cause least terns and snowy plovers to abandon the existing nesting areas 

on the Refuge. A management strategy that excludes any form of predator management 

would place the viability of the Refuge’s listed species at risk and would be inconsistent with 

the purposes for which this Refuge was established. 

 

X. Justification 

The implementation of this predator management plan will result in temporary localized 

reductions in populations of some mammalian and native avian predators around the Refuge. In 

recent years, the California ground squirrel, Norway rat, and black rat were the mammalian 

species most affected by predator management, while ravens and western gulls were the avian 

species most often removed from nesting areas. The lethal removal of some raptors and large 

native mammalian predators will occur annually on the Refuge, however the numbers of 

individuals lost will be low (one to three annually). Lethal removal will generally only be 

implemented after other non-lethal methods for removal and relocation have proved to be 

unsuccessful. For the most part, avian predators, with the exception of corvids and some gulls, will 

be trapped and released into suitable habitat elsewhere, and only those avian predators that are 

foraging within nesting areas will be removed. 

The Federal endangered and threatened avian species supported by these Refuges were once 

more widely distributed throughout southern California and the sizes of the various populations 

throughout the region were much larger. The loss of coastal habitat, displacement of nesting areas 

due to increasing human use of beaches and surrounding wetlands, increases in non-native 

predators in proximity to natural areas, and the concentration of native predators into smaller, 

more isolated natural areas have all contributed to significant declines in the populations of 

California least tern, western snowy plover, and light-footed clapper rail. The recovery plans 

prepared for the Refuge’s Federal endangered and threatened species (USFWS 1985a, 1985b, 

1998, 2001, 2002), as well as the conservation plans prepared to address declines in the populations 

of shorebirds and waterbirds (Page et al. 2003 and Kushlan et al. 2002), all include predator 

control in the list of recovery and conservation actions that must be considered if reversal of these 

population declines is to be achieved. However, predator control alone cannot achieve the recovery 

goals established for these species, which is why this predator management plan is just one 
───────────────────────────────────────────── Appendix M

───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 17

component of a larger overall management plan for the Refuge. The CCP for this Refuge includes 

habitat enhancement and restoration proposals, as well as additional actions directed at reducing 

disturbance to sensitive species. Through this combination of efforts, the Refuge’s populations of 

endangered and threatened species are expected, at a minimum to sustain their current sizes, and 

ideally to increase as these various actions are implemented. 

X. References Cited

California Coastal Commission. 1987. The California Coastal Resource Guide. University of 

California Press. 

Densmore, Robin J. 1990. Gull-billed Tern Predation on a Least Tern Chick. Wilson Bulletin 

102(1): 180-181. 

Hickey, C., W.D. Shuford, G.W. Page, and S. Warnock. 2003. Version 1.1. The Southern Pacific 

Shorebird Conservation Plan: A strategy for supporting California’s Central Valley and coastal 

shorebird populations. PRBO Conservation Science, Stinson Beach, CA. 

Jaques, D. and D. Anderson. 1987. “Conservation Implications of Habitat Use and Behavior of 

Wintering Brown Pelicans (Pelecanus occidentalis californicus).” Final Report to Public Service 

Research and Dissemination Program University of California, Davis, California. 

Kushlan, J.A., J. Steinkamp, K.C. Parsons, J. Capp, M. Acosta Cruz, M. Coulter, I. Davidson, L. 

Dickson, N. Edelson, R. Elliot, R. M. Erwin, S. Hatch, S. Kress, R. Milko, S. Miller, K. Wheeler, 

and K. Wohl. 2002. Waterbird Conservation for the Americas: The North American Waterbird 

Conservation Plan, Version 1. Waterbird Conservation for the Americas, Washington, DC, U.S.A. 

Palacios, Eduardo and Eric Mellink. 2003. Status, Distribution, and Ecology of Nesting Larids in 

Western Mexico, with Emphasis on Vanrossemi Gull-billed Terns and Caspian Terns – Final 

Report. (Draft, November 2003) 

Patton, Robert. 2001. The Status of Western Gull-billed Terns at South San Diego Bay National 

Wildlife Refuge in 2001. 

Patton, Robert. 2002. California Least Tern Breeding Survey 2000 Season. Final Report to the 

State of California Department of Fish and Game. 

Patton, Robert. 2004. The Status of Western Gull-billed Terns at South San Diego Bay National 

Wildlife Refuge in 2003. 

Powell, A.N., C.L. Fritz, B.L. Peterson, and J.M. Terp. 2002. “Status of Breeding and Wintering 

Snowy Plovers in San Diego County, California, 1994 – 1999.” Journal of Field Ornithology 

73(2):156-165. 

U.S. Fish and Wildlife Service. 1983. The California Brown Pelican Recovery Plan. 

U.S. Fish and Wildlife Service. 1985a. California Least Tern Recovery Plan. 

U.S. Fish and Wildlife Service. 1985b. Light-footed Clapper Rail Recovery Plan. 
Appendix M ────────────────────────────────────────────── 

18 ───────────── Final Predator Management Plan - San Diego Bay National Wildlife Refuge 

U.S. Fish and Wildlife Service. 2001. Western Snowy Plover (Charadrius alexandrinus nivosus) 

Pacific Coast Population Draft Recovery Plan. (May 2001) 

U.S. Fish and Wildlife Service. 2002. Birds of Conservation Concern 2002. Division of Migratory 

Bird Management, Arlington, Virginia (December 2002). 

U.S. Fish and Wildlife Service. 2003. Draft Comprehensive Conservation Plan/Environmental 

Impact Statement for the Sweetwater Marsh National Wildlife Refuge and the South San Diego 

Bay Unit of the San Diego National Wildlife Refuge. San Diego National Wildlife Refuge 

Complex, Carlsbad, CA. 
 

Appendix N 

Wilderness Inventory 
───────────── Final Comprehensive Conservation Plan/Environmental Impact Statement N-1

Appendix N: Wilderness Inventory

Introduction

The purpose of a wilderness review is to identify and recommend for Congressional designation 

National Wildlife Refuge System (System) lands and waters that merit inclusion in the National 

Wilderness Preservation System (NWPS). Wilderness reviews are a required element of 

comprehensive conservation plans (CCPs) and conducted in accordance with the refuge planning 

process outlined in 602 FW 1 and 3, including public involvement and the National Environmental 

Policy Act (NEPA) compliance. 

There are three phases to the wilderness review: 1) inventory, 2) study; and 3) recommendation. 

Lands and waters that meet the minimum criteria for wilderness are identified in the inventory 

phase. These areas are called wilderness study areas (WSAs). WSAs are evaluated through the 

CCP process to determine their suitability for wilderness designation. In the study phase, a range 

of management alternatives are evaluated to determine if a WSA is suitable for wilderness 

designation or management under an alternate set of goals and objectives that do not involve 

wilderness designation. The recommendation phase consists of forwarding or reporting 

recommendations for wilderness designation from the Director through the Secretary and the 

President to Congress in a wilderness study report. 

If the inventory does not identify any areas that meet the WSA criteria, we document our findings 

in the administrative record for the CCP, fulfilling the planning requirement for a wilderness 

review. We inventoried Service lands and waters within the Sweetwater Marsh and South San 

Diego Bay Units of the San Diego Bay NWR and found no areas that meet the eligibility criteria 

for a WSA as defined by the Wilderness Act. This appendix summarizes the wilderness inventory 

for the Sweetwater Marsh and South San Diego Bay Units of the San Diego Bay NWR. 

Inventory Criteria

The wilderness inventory is a broad look at the planning area to identify WSAs. These are 

roadless areas that meet the minimum criteria for wilderness identified in Section 2(c) of the 

Wilderness Act. 

"A wilderness, in contrast with those areas where man and his works dominate the 

landscape, is hereby recognized as an area where the earth and its community of life are 

untrammeled by man, where man himself is a visitor who does not remain. An area of 

wilderness is further defined to mean in this Act an area of undeveloped Federal land 

retaining its primeval character and influence, without permanent improvements or human 

habitation, which is protected and managed so as to preserve its natural conditions, and 

which: (1) generally appears to have been affected primarily by the forces of nature, with the 

imprint of man’s work substantially unnoticeable; (2) has outstanding opportunities for 

solitude or a primitive and unconfined type of recreation; (3) has at least five thousand acres 

of land or is of sufficient size as to make practicable its preservation and use in an 

unimpaired condition; and (4) may also contain ecological, geological or other features of 

scientific, educational, scenic, or historical value." 
Appendix N ──────────────────────────────────────────────

 N-2 San Diego Bay National Wildlife Refuge ───────────────────────────────

A WSA must be a roadless area or island, meet the size criteria, appear natural, and provide 

outstanding opportunities for solitude or primitive recreation. The process for identification of

roadless areas and islands in the Sweetwater Marsh and San Diego Bay Units and application of 

the wilderness criteria are described in the following sections. 

Identification of Roadless Areas and Roadless Islands

Identification of roadless areas and roadless islands required gathering and evaluating land status 

maps, land use and road inventory data, and aerial photographs for the Sweetwater Marsh and 

South San Diego Bay Units. “Roadless” refers to the absence of improved roads suitable and 

maintained for public travel by means of motorized vehicles primarily intended for highway use. 

Only lands currently owned by the Service in fee title were evaluated. 

Evaluation of the Size Criteria

Roadless areas or roadless islands meet the size criteria if any one of the following standards 

apply:

• An area with over 5,000 contiguous acres. State and private lands are not included in 

making this acreage determination. 

• A roadless island of any size. A roadless island is defined as an area surrounded by 

permanent waters or that is markedly distinguished from the surrounding lands by 

topographical or ecological features. 

• An area of less than 5,000 contiguous Federal acres that is of sufficient size as to make 

practicable its preservation and use in an unimpaired condition, and of a size suitable for 

wilderness management. 

• An area of less than 5,000 contiguous Federal acres that is contiguous with a designated 

wilderness, recommended wilderness, or area under wilderness review by another Federal 

wilderness managing agency such as the Forest Service, National Park Service, or Bureau 

of Land Management. 

Evaluation of the Naturalness Criteria

In addition to being roadless, a WSA must meet the naturalness criteria. Section 2(c) defines 

wilderness as an area that “... generally appears to have been affected primarily by the forces of nature 

with the imprint of man’s work substantially unnoticeable.” The area must appear natural to the 

average visitor rather than “pristine.” The presence of historic landscape conditions is not required. 

An area may include some human impacts provided they are substantially unnoticeable in the unit as a 

whole. Significant human-caused hazards, such as the presence of unexploded ordnance from military 

activity, and the physical impacts of refuge management facilities and activities are also considered in 

evaluation of the naturalness criteria. An area may not be considered unnatural in appearance solely 

on the basis of the “sights and sounds” of human impacts and activities outside the boundary of the 

unit. 

 

Evaluation of Outstanding Opportunities for Solitude or Primitive and Unconfined Recreation

In addition to meeting the size and naturalness criteria, a WSA must provide outstanding 

opportunities for solitude or primitive recreation. The area does not have to possess outstanding 

opportunities for both solitude and primitive and unconfined recreation, and does not need to have 

outstanding opportunities on every acre. Further, an area does not have to be open to public use and 
Appendix N ────────────────────────────────────────────────

────────────── Final Comprehensive Conservation Plan/Environmental Impact Statement N-3

access to qualify under this criteria; Congress has designated a number of wilderness areas in the 

Refuge System that are closed to public access to protect resource values. 

Opportunities for solitude refer to the ability of a visitor to be alone and secluded from other visitors in 

the area. Primitive and unconfined recreation means non-motorized, dispersed outdoor recreation 

activities that are compatible and do not require developed facilities or mechanical transport. These 

primitive recreation activities may provide opportunities to experience challenge and risk; self reliance; 

and adventure. 

These two "opportunity elements” are not well defined by the Wilderness Act but, in most cases, can be 

expected to occur together. However, an outstanding opportunity for solitude may be present in an 

area offering only limited primitive recreation potential. Conversely, an area may be so attractive for 

recreation use that experiencing solitude is not an option. 

Evaluation of Supplemental Values 

Supplemental values are defined by the Wilderness Act as “...ecological, geological, or other features of 

scientific, educational, scenic, or historic value.” These values are not required for wilderness but their 

presence should be documented. 

Inventory Findings 

As documented below, none of the parcels in the Sweetwater Marsh or South San Diego Bay Units of 

the San Diego Bay NWR meet the criteria for a WSA. 

Roadless Areas and Roadless Islands 

The Sweetwater Marsh Unit includes an access road that accommodates motorized access to both the 

Chula Vista Nature Center and the Refuge office. This road, although gated and not available for 

travel by the general public, is used to transport the public to and from the Nature Center and Refuge 

via a bus. No public roads are located within the portion of the South San Diego Bay Unit that is 

owned by the Service in fee title. 

Size Criteria

A total of 316 acres of Service owned-land are included within the Sweetwater Marsh Unit. The 

majority of the 2,324 acres of land included within the current boundary of the South San Diego Bay 

Unit is leased to the Service from the State of California for management as a National Wildlife 

Refuge. Approximately 90 acres of the Refuge are owned by the Service in fee title. No islands are 

included within the San Diego Bay NWR. 

Naturalness Criteria

The marsh habitat within the Sweetwater Marsh Unit appears natural to the refuge visitor. However, 

the upland area on Gunpowder Point, which was the site of industrial and agricultural activity for many 

decades prior to the establishment of the Refuge, continues to include evidence of these past activities 

and supports a mix of exotic plants, weedy invasive plants, and some native shrubs. The Otay River 

floodplain portion of the South San Diego Bay Unit was also farmed for several decades and currently 

supports weedy vegetation that would not appear natural to the refuge visitor. Also included within 

this Unit is an active commercial solar salt operation. 
Appendix N ──────────────────────────────────────────────

 N-4 San Diego Bay National Wildlife Refuge ───────────────────────────────

Outstanding Opportunities for Solitude or Primitive and Unconfined Recreation 

The San Diego Bay NWR is located immediately adjacent to the urbanized communities of National 

City, Chula Vista, San Diego, Coronado, and Imperial Beach. Although the Refuge does provide 

opportunities for escape from the urban environment, the sites and sounds of urbanization are always 

present just beyond the Refuge boundary. 

Supplemental Values 

The San Diego Bay NWR includes portions of San Diego Bay, which provides significant scenic value 

to visitors of the Refuge and the surrounding communities. The undisturbed salt marsh habitat on the 

Sweetwater Marsh Unit also provides scenic and regionally significant ecological value.
 

Appendix O 

 Letter from the California 

Department of Fish and Game
───────────── Draft Comprehensive Conservation Plan/Environmental Impact Statement O-1

 Appendix O: Letter from the California 

Department of Fish and Game 
Appendix O ──────────────────────────────────────────────

O-2 San Diego Bay National Wildlife Refuge ─────────────────────────────── 
San Diego Bay National Wildlife Refuge

San Diego Bay National Wildlife Refuge Complex

6010 Hidden Valley Road

Carlsbad, CA 92011

Telephone: 760/930 0168

Fax: 760/930 0256

California Relay Service

TTY 1 800/735 2929

Voice 1 800/735 2922

U.S. Fish & Wildlife Service

http://pacific.fws.gov

For Refuge information

1 800/344 WILD

August 2006

Photo: USFWS/J. Konecny