San Diego Bay


Site San Diego Bay. 6 wetland areas scattered around the margins of the south Bay.

Map Imperial Beach, National City, and Point Loma USGS 7.5' quadrangles.

Location 5 miles north of border with Mexico, surrounded by cities of San Diego, Coronado, National City, Chula Vista and Imperial Beach; remaining intertidal habitat is primarily in the south Bay.

Contacts US Fish and Wildlife Service, Carlsbad (619) 431-9440.

Chula Vista Nature Center (619) 422-2473.

To be provided

Approximate Wetland Habitat Acreage 2,299 acres fragmented among 6 areas of the south Bay
9, 13, 17
Approximate Historic Acreage 6,730

Ownership Owner Acres Source

San Diego Unified Port District. Acreage is for granted tidelands of the entire Bay. These areas include the Chula Vista Wildlife Reserve, Telegraph Cr/J Street marsh, as well as eelgrass beds and mudflats. 5,483 5

State Lands Commission. Acreage is for salt ponds and eelgrass beds. 600 + 4

US Fish and Wildlife Service. Sweetwater Marsh NWR acreage includes approximately 225 acres of salt marsh, as well as mudflats and uplands. 315.8 10

US Navy. Acreage includes the South Bay Biological Study Area salt marsh and seasonal wetlands and salt flats in the Naval Radio Receiving Facility. 113 17

Private. A portion of the salt works. 850 4


Land Use Designation San Diego Unified Port District Master Plan 1993 update - most wetland areas are designated for conservation uses allowing little or no development. Some mudflats on the western shore are designated Recreation, Navigation.
5, 6

Various low intensity designations surround the Otay River channel.

Onsite Use The Bay supports a major international port, high-intensity uses occurring mostly in the north; uses include: shipping, US Naval facilities, an international airport, water-oriented recreation, commerical fishing, a power plant, salt production,
5, 1, 9, 10, 18

and flood control channels, as well as roadways on fill. There is also a National Wildlife Refuge with an interpretive center. The South Bay Biological Study Area provides a site for birdwatching and is the terminus of a bike trail.

Historic Use Port activities began in 1850; the San Diego River was diked in 1877, permanently excluding its flows from the Bay; salt production began in 1902; the Bay received sewage and industrial waste until 1963; the Bay and shoreline have been modified by

extensive dredging and filling.

Adjacent Use The Bay is entirely surrounded by development of 5 cities; open spaces include Balboa Park/San Diego Zoo complex, portions of Sweetwater and Otay River corridors.
1, 14
Historic Adjacent Use Gradual urbanization to the present


Tidal Influence The Bay shoreline is fully tidal, although circulation in south bay is described as poor; the Sweetwater River, Paradise Creek, and the Connector marsh are all culverted; a flood control channel parallel to the Sweetwater River conveys tidal flow inland.
9, 3, 23, 13

Tidal influence reaches 2.5 miles up the Otay River.

Watershed Area 415 sq miles

Tributaries and Flow Tributary Flow Source

Sweetwater River A concrete flood control channel runs parallel to the river outlet and diverts high flows; the natural corridor is connected to the channel just east of Broadway. No flow rates specified. 2

Otay River Significant flows occur only when the dam spills, this happened 17 times between 1927 and 1983; a 1974 estimate of the 10-yr peak flow rate was 3,700 cfs, the 100-yr estimate was 22,000 cfs; the river is diked between the salt ponds. 13

Paradise Creek A small stream, it is partially channelized, and culverted under I-5. 2
Dams 2 each on Sweetwater and Otay rivers. The Sweetwater reservoir was built in 1888; the Savage Dam on Otay river was built in 1919 and controls 69% of the watershed.
Other Sources Major storm drains are located at the Chula Vista boat basin, and at the foot of J and L streets.


General Power plant cooling, dammed tributaries and contaminants from urban runoff all affect water quality; the Bay is characterized as having recovered from many severe pollution problems which were addressed by the late 60s.
9, 20, 21, 22

The North and South Bay were listed as impaired in 1994; the draft list for 1996 indicates criteria for copper exceeded in the north Bay. Designated benefical uses: ind, nav, rec1, rec2, comm, biol, est, wild, rare, mar, migr, shell.

Dissolved Oxygen (DO) 1979-80 study of the south Bay reported Aug bottom readings ranging 3.8-12.3 mg/l; surveys done during 1986-88 were reported as having found similar concentrations. Neither time of sampling nor temperature were specified in the source document.
Water Salinity 1977-80 study of the south Bay reported Aug bottom readings ranging from 33.4 - 37.2 ppt; other characteristics reported - evaporation exceeds freshwater inflow in the summer, and vertical salinity gradients are evident in winter.
Sediment Sediment deposition occurs episodically, with flooding of tributaries; fine marine sediments are carried into south Bay mainly through tidal action.


Soil Bay muds 5-20 ft deep overlay sand and consolidated sedimentary deposits; the Connector marsh, D St fill marsh, and Chula Vista Wildlife Reserve are all created from dredged material.
9, 3, 8

Habitat Acres Vegetation Source
Eelgrass. 1993 acreage for the entire Bay 1260 Eelgrass and associated algae 9, 19
Intertidal Sand/Mudflat. Acreage is for the south Bay; flats occur along margins of most of the south Bay, with the exception of Coronado Cays on the western shore and Chula Vista Marina on the east. 658 July 1988-1989 - species encountered by subtidal grab and intertidal mudflat core samples - several species of green algae, red algae, and Sea Lettuce together in dense mats. 9
Salt marsh. Acreage covers: Sweetwater marsh complex, the J Street marsh, the Chula Vista Wildlife Reserve, the South Bay Biological Study Area and small areas of the Otay River Channel. approx 300 1987-84 - A total of 17 native salt marsh species was identified at all areas, including cordgrass at all but the Otay River channel; cordgrass at Chula Vista Reserve was transplanted from marsh north of D St. fill. ac., 9, 13 plants, 3, 8, 13, 9, 23

1994 - Salt marsh bird's beak+ (re-established population) at the Sweetwater marsh.
Freshwater/ brackish marsh. Identified in a small area between the Otay river channel and I-5. 2.9 1987 - Pickleweed, bulrush, San Diego marsh-elder+, cattail present 6, 13
Seasonal wetlands. At the Naval Radio Receiving Station 19 1989 report indicated variation among the depressions; curly dock, alkali-mallow, small-flowered ice plant*, sedge, cattail*, and pepper-tree* listed. 200 plants of salt marsh bird's beak+ also identified in 1995. ac., 17 plants, 18
Salt flats. At the Naval Radio Receiving Facility 67 1989 report identified pickleweed as the dominant species; pineapple-weed, small-flowered ice plant* and woolly marbles also present, as well as variegated dudleya+ in association with coast barrel cactus+, and coast cholla in "significant stands". ac., 17 plants, 9, 17
Transition - at the Sweetwater Refuge complex and a disturbed area adjacent to South Bay Biological Study Area Not specified 1990 - includes saltgrass, alkalai heath, Palmer's frankenia; species adjacent to So Bay Study Area not specified, 1989 report indicated that the area was used for a parking lot. 9, 10
Upland - present at: Sweetwater Refuge complex, Chula Vista Reserve, adjacent to Telegraph Ck/J St marsh, Naval Radio Receiving Facility and between the Otay River channel and I-5. Acreage estimated from various sources 400 + 1987, 1990 - coastal sage scrub at Sweetwater marsh complex and disturbed fields near Otay river; coastal dunes, grassland and disturbed scrub at the Naval Radio Receiving Facility. ac., 9, 10, 13 plants, 9, 10, 13, 17
Salt ponds 1,252 Not specified 9


Birds 1993-1994 - weekly surveys of central, south bay, and the salt works found 104 species - 95 water-associated, 9 raptor, 25 sensitive including 9 breeding. A total of 522,553 birds recorded during the salt work survey.
1, 4, 13
Fish July 1993 Sweetwater complex - arrow goby and Ca killifish were dominants of the natural channels; topsmelt, Ca killifish and longjaw mudsucker were dominant species in the constructed channels. Yellowfin goby*, and sailfin molly*
3, 8, 9

prevalent in both. 1989 Chula Vista Rsve flume survey found the same dominant species. 1988-89 seines of so. bay intertidal area and tidal creeks found 31 species, arrow goby, topsmelt, round stingray, staghorn sculpin were most abundant.

Benthic Invertebrates 1988-89 cores of the south bay intertidal - Oligochaete sp., Polydora ligni*, Capitella capitata, Scolelepsis acuta had the highest avg annual densities. 1994 Sweetwater complex - 9 species found in natural channels, 22 in the
9, 3

constructed; Japanese mussel* common in both, but 6x more abundant in constructed channels; oriental shrimp* also common in constructed channels; abundance of 3 crabs preferred by light-footed clapper rail was similar in both.

Insect 1990 Chula Vista Reserve - Coleomegilla fuscilabris beetles introduced to control Haliaspis,Spartina, scale, predation on occurred but the scale was still abundant after 1 year; 2 types of ladybugs observed at the Rsv and Paradise Ck.
Other Wildlife 1990 Sweetwater complex - San Diego coast horned lizard+ in marsh-upland transition; San Diego alligator lizard, San Diego horned lizard, Great Basin fence lizard, San Diego gopher snake, Ca king snake also present on Refuge.
10, 6, 9

Hammond two-striped garter snake+ sighted in 1988 survey of lower Otay River; pre-1980 survey found Yosemite toad, Ca tree frog, Pacific chorus frog, bullfrog, and raccoon all in salt marsh. 1989 report cites seasonal presence of sea turtles in south Bay.

Special Status Species Salt marsh bird's beak, variegated dudleya, coast barrel cactus, Ca gull, Ca least tern#, elegant tern#, black tern, gull-billed tern#, west snowy plover#, long-billed curlew, light-footed clapper rail#, black skimmer#, reddish egret,
10, 6, 1, 4, 15, 17

common loon, western grebe, Clark's grebe, double-crested cormorant#, Ca brown pelican, osprey, peregrine falcon, northern harrier, Belding's Savannah sparrow#, large-billed Savannah sparrow, Ca horned lark#, sharp-shinned hawk, Cooper's hawk, merlin,

burrowing owl, short-eared owl, Hammond two-striped garter snake.


Enhancement Status Creation of the approximately 60-acre Chula Vista Wildlife Reserve from dredged material began in 1970. In 1984 Paradise Creek was reopened, the dredged material "Connector Islands" were created, and in 1985 cordgrass planting was initiated on the
9, 8, 7, 6, 2,13, 16,18, 23

islands. Eelgrass was planted in 1988 along the north side of the Chula Vista Rsve. An enhancement plan was prepared in 1989 focusing on intertidal habitats of the south bay. 17 acres of the "D Street fill" were excavated and planted with salt marsh

species 1990-91. Consideration is being given to establishing a National Wildlife Refuge in the southern most portion of the bay. The Navy regularly updates management plans for protection of natural resources on the Radio Receiving Facility.

Watershed Management A plan is being developed for an Otay River Valley Regional Parkway to: provide recreation and protect environmentally sensitive areas, cultural and compatible agricultural resources; the area extends 13 miles inland and includes side canyons.

A Habitat Conservation Plan was finalized in 1991 for least Bell's vireo habitat along the Sweetwater River west of the Loveland Reservoir; a concept plan has been developed for a National Wildlife Refuge planning area for approximately 44,800
12, 16

acres of the Sweetwater and Otay River watersheds.

Pressure Continued modification of water quality by power plant intake and discharge; increased demand for commerce, recreation, waterfront development in the Bay; continued urbanization of surrounding watersheds,
9, 5, 4

the 1994 resources report listed 26 proposed/approved developments in the Otay Valley.



1 Manning, J.A. 1995. Waterbirds of Central and South San Diego Bay 1993 -1994. U.S. Fish and Wildlife Service, Coastal Ecosystem Program. 45 pp. and appendices.

One-year investigation of waterbird species richness, composition, and distribution across open water habitats in central and southern San Diego Bay. Report discusses bird survey methods, interprets results, and evaluates the area's

relative regional significance for migratory birds. Makes recommendations for land-use planning, habitat restoration and enhancement, and research. Technical appendices include cumulative waterbird counts, and maps and text

describing the occurrence, high use areas, and distributions of waterbirds in the region.

2 Martin Kenney, U.S. Fish and Wildlife Service, Carlsbad. Personal communication July 12, 1995.

3 Pacific Estuarine Research Laboratory (PERL). 1994. Final Sweetwater Marsh Wetland Complex Ecosystem Assessment. Annual report of the California Dept. of Transportation.

A summary of six years of monitoring results at the Sweetwater Marsh wetland complex. The object of the program is to assist CalTrans and USFWS in assessing the restoration sites at Sweetwater River Wetland Complex. The monitoring

program compares parameters in natural and constructed communities of the marsh complex for water quality, soil salinity, species composition of low, medium, and high intertidal communities, and fish and invertebrates in channels.

4 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 Ecosystem Program. 25 pp. and appendices.

Results of a one-year survey of water associated birds within and adjacent to a salt extraction facility in south San Diego Bay. Technical appendices describe operations of salt works, and contain maps of abundance, occurrence,

and distribution of bird species.

5 San Diego Unified Port District. Port Master Plan. Revised May 1993. 140 pp. and appendix.

Provides the Port District's official planning policies for the physical development of the tide and submerged lands within its jurisdiction. "Precise plans" are provided for each of the Port District's nine planning districts.

San Diego Bay is within the PortŐs planning jurisdiction. Approximately 37 percent of the tidelands on the Bay have been granted to the Port District. Over a dozen background reports are incorporated into the Plan.

6 California State Coastal Conservancy and the City of Chula Vista. 1992. Otay River Valley resource enhancement plan. 110 pp. and appendices.

A planning document to guide the preservation and enhancement of natural resources and open space for the Otay Valley west of Otay Valley Road. Outlines goals, describes implementation options, and discusses public financing opportunities.

and cultural resource analyses using existing data. Prepared by Wallace, Roberts and Todd.

7 Zedler, J. B. and R. Langis. 1991. Comparisons of constructed and natural salt marshes of San Diego Bay. Restoration and Management Notes 9:1. 5 pp.

Evaluation of the California Dept. of Transportation's marsh mitigation project at the "Connector Marsh," part of Sweetwater Marsh National Wildlife Refuge. The report summarizes a study conducted from 1987 to 1988 comparing cordgrass

height, epibenthos organism density, and exotic species occurrence at the Connector Marsh and a natural marsh, Paradise Creek Marsh. The report also identifies deficiencies in the Connector Marsh and summarizes results of 1990 field

experiments that tested possible causes and remedies of those deficiencies.

8 Entrix, Inc. and Pacific Estuarine Reserach Laboratory. 1991. Chula Vista Wildlife Reserve studies: vegetation, scale insect control, and fish. 59 pp. and appendix.

Compilation of four studies of constructed wetlands from 1989 to 1990: a photographic survey of marsh development, a quantitative vegetation study, a final report on scale insect control experiments, and a final report on an

assessment of fish use of the marsh and mudflats. Reports prepared for the Port of San Diego. Appendix contains photographs taken during survey.

9 San Diego Unified Port District and the California State Coastal Conservancy. 1989. South San Diego Bay enhancement plan. Four volumes. 490 pp. and appendices.

Includes review of existing literature on natural resources values of area, comprehensive field inventory of natural resources emphasizing invertebrates, fish, birds, and additional studies of saltmarsh habitats, eelgrass resources, and

selected environmental variables. Prepared by Michael Brandman Associates. Appendices compile data from field studies.

10 U.S. Fish and Wildlife Service. 1990. Sweetwater Marsh National Wildlife Refuge, Chula Vista, California: annual narrative report, calendar year 1990. 18 pp.

Report summarizing activities at SMNMR for year 1990. Reports on creation of reserve, management activities, public participation, compliance with laws and the terms of a stipulated settlement agreement, research conducted on reserve, habitat types,

mosquito control activities, and endangered plant and wildlife.

11 County of San Diego Department of Parks and Recreation. 1994. Final Otay River Valley resources report. Approx 200 pp.

An inventory of existing documents on land use, biology, cultural resources and hydrology within the Otay River Valley Focused Planning Area - the River valley from Lower Otay Lake to San Diego Bay and all drainages. The existing information

provides the basis for a description of the area's resources, an evaluation of the data's adequacy for planning and environmental review, and identification of issues and recommendations for developing a regional park plan. Prepared by Lettieri-McIntyre.

12 San Diego Association of Governments. 1991. Revised Final Sweetwater River Habitat Conservation Plan. 213 pp.

The Habitat Conservation Plan (HCP) is part of the Comprehensive Species Management Plan (CSMP) for the endangered least Bell's vireo. The HCP identifies riparian habitat to be protected, conserved, managed, and reclaimed to ensure protection

and recovery of the species within the focused planning area. This area generally includes the 100-yr floodplain plus a 150-foot buffer of the Sweetwater River from San Diego Bay to the Loveland Reservoir. Based on 1987 CSMP surveys.

13 Southwest Wetlands Interpretive Association and The California State Coastal Conservancy. 1989. Lower Otay River Wetlands Enhancement Plan. 162 pp and technical appendices.

A conceptual plan for increasing the area of salt marsh and riparian woodland, protecting endangered species habitat and providing for compatible public access at a 133-acre site adjacent to the lower Otay River and San Diego Bay. Study

includes an assessment of existing conditions with regard to geology, surface water hydrology, biology and land use, as well as an opportunities and constraints analysis. Based on existing information and field surveys.

14 State Coastal Conservancy. 1989. The coastal wetlands of San Diego County. 64 pp.

Public education booklet describing ecological concepts and dynamics of San Diego County salt marshes. Discussion includes watershed processes, littoral and tidal influences, habitat types, significance to migratory

birds, and the effects of urban development. Profiles the history, current values and problems, protection efforts and public access opportunities at 13 wetland areas.

15 Zembal, Richard. 1995. Status and distribution of light-footed clapper rails in California, 1980-1995. Preliminary report to the California Department of Fish and Game. 28pp.

Results of the 1995 survey of breeding light-footed clapper rails in California. The report incorporates data from 15 years of annual surveys and disusses population trends for the region and at each of 36 sites censused. Trends are tied to

ecological conditions at each site and the author identifies possibilities for improving habitat.

16 U.S. Fish and Wildlife Service. 1995. Proposal for Wildlife Habitat Protection, Concept Plan for San Diego National Wildlife Refuge. 18 pp.

Developed as part of the U.S. Fish and Wildlife Service's contribution to the Multiple Species Conservation Program in the San Diego region, the plan sketches out the Service's proposal to establish the San Diego National Wildlife Refuge which would

consist of several units. Planning areas cover portions of the Otay and Sweetwater watersheds, vernal pool areas and south San Diego Bay. The plan describes the subject habitats as well as the planning process and avenues for public participation.

17 U.S. Fish and Wildlife Service. 1989. Fish, wildlife, and habitat management plan for Naval Radio Receiving Facility Imperial Beach, California. 57 pp.

The plan describes the plant communities, animals and habitats present at the facility, anticipates potential impacts associated with facility operations (negligible) and recommends actions for habitat improvement. It is

based on contemporary field surveys and a resource inventory from 1982. The report includes a list of plant and wildlife species known to occur at the facility. It is incorporated as Appendix F to the facility's 1989 Natural Resource Management Plan.

18 Edie Jacobsen, Southwest Division, Naval Facilities Engineering Command. Personal communication, October 17, 27, 1995.

19 Perdue, Mitchell. 1994. San Diego Bay eelgrass final survey charts, correspondence from Southwest Division, Naval Facilities Engineering Command to San Diego Bay Eelgrass Working Group, April 18, 1994. 2pp.

A memo briefly describing the purpose, scope, methods of the Navy's hydrographic and eelgrass mapping surveys for San Diego Bay. The availability of project results and preliminary results are also mentioned.

20 San Diego Regional Water Quality Control Board. 1994. Water quality control plan for the San Diego basin. Approximately 225 pp. and appendices.

The plan designates beneficial uses and associated water quality objectives for inland surface waters, coastal waters, reservoirs and lakes and ground water in San Diego County. It includes a discussion of applicable policies and statutory

requirements and identifies measures for achieving water quality objectives. It also describes ongoing monitoring and assessment programs. Appendices contain summaries of regional growth forecasts and criteria for organic and inorganic constituents.

21 State Water Resources Control Board. 1994. List of impaired water bodies.

Developed as part of the Water Quality Assessment of the State's major waterbodies. Separate lists are developed to rate waterbodies as Good, Intermediate, Impaired or Unknown Quality. Impaired waters are those not expected to attain or maintain

water quality standards. The state list is a compilation of those developed by the nine regional boards. Lists of impaired water bodies are also known as 303(d) lists as they meet a requirement of section 303(d) of the federal Clean Water Act.

22 San Diego Regional Water Quality Control Board. 1996. Draft 303(d) list.

A proposed list of waterbodies in the San Diego Basin that do not or are not expected to attain water quality standards after application of required technology-based controls. Specifies selected beneficial uses and criteria assessed,

and the percentage of samples in which criteria were exceeded. It also identifies waterbodies for which previous assessments are no longer applicable.

23 Joy Zedler, San Diego State University, Pacific Estuarine Research Laboratory. Personal communication December 5, 1995.

24 MEC. 1993. San Dieguito Lagoon restoration project regional coastal lagoon resources summary. 56 pp and appendix.

This report provides a summary of habitat types, fish, bird and benthic invertebrate populations at 16 coastal wetlands south of Anaheim Bay. It is a synopsis of primarily existing information; sources used in identifying and quantifying

habitat types include aerial photographs taken in early 1993. Identification of wetland habitats in San Diego Bay includes Sweetwater Marsh Complex only. Discusses restoration of habitats at San Dieguito Lagoon given present and historic

conditions of other coastal wetlands in the region. This report was prepared as part of the San Dieguito Restoration Project undertaken by Southern California Edison to mitigate for damage to coastal marine resources from the

operation of the San Onofore Nuclear Generating Station.



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