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faces the threats of continued sedimentation, continued urban development in the watershed, proposed re-alignment and widening of Carmel Valley and Sorrento Valley roads, and exotic vegetation and fauna. Developments outside the coastal zone cause problems in the lagoons and marshes of the subregion. Few restoration and conserva-tion plans are devoted to upper watershed issues and threats posed by land-use activity.

Mission Bay (Rose Creek, Tecolote Creek)

Historically, False Bay encompassed over 5,000 acres and was once a deep-water embayment. Marshes and mudflats extended from the southeastern shore of False Bay to the northeastern shore of San Diego Bay.

False Bay became a small-craft harbor and recreation area in the late 1940s, when the COE began dredging the bay and rerouting the river. The final reconfiguration of False Bay into Mission Bay Park led to large-scale loss of fragile wetlands and marshes. Only two remnants of the natural marsh remain, Kendall Frost Marsh Preserve and Famosa Slough.

There are approximately 251 acres of wetland habitat in the Bay, includ-ing 41-acres in the Northern Wildlife Preserve (includes Kendall-Frost Reserve), about 200 acres in the Southern Wildlife Preserve (San Diego River channel), and approximately 10 acres of created salt pan. Before development and the filling in of the Bay, the Bay included approximately 3,335 acres of wetlands. As with most Bays in the South Coast, the wetlands have been degraded or lost. There are 4 dams within the San Diego River watershed: El Capitan on the main river; San Vicente, Lake Jennings, and Cuyamaca on tributaries. Runoff from approximately 10 square miles of the watershed is conveyed to the bay over the shoreline and through storm drains. There are 69 storm drains that enter the bay, 3 of those into the Northern Wildlife Preserve.

Mission Bay is an intensively used multi-use area with hotels, marinas, theme parks, and beaches, among other attractions. A rip-rapped chan-nel connects the Bay and the Ocean. The Bay is irregularly shaped, with 2 large islands and depths ranging 7-20 feet. Circulation in the bay is poor in the eastern portion. The Northern and Southern Wildlife Preserves are tidally influenced. Sand bars may inhibit tidal flow at the Southern Preserve.

A 1994 report characterized the bay’s primary water quality problem as contamination from urban runoff combined with poor tidal flushing. The bay was listed in 1994 as an impaired water body.

The bay contains three types of aquatic habitats – sandy bottom shallow water, eelgrass beds and rocky shoreline, and two types of intertidal habitats – mudflat and marsh. The aquatic habitat supports over 25 species of marine fish and numerous invertebrates (California Coastal Conservancy 1989). Biological surveys in 1988 found 92 species of which 70 were water-associated and 7 special status species, including nesting California least tern, light-footed clapper rail, Belding’s Savannah sparrow, western snowy plover, California brown pelican, peregrine falcon, California gull, and California horned lark. A great blue heron rookery was also found. Twenty species were identified in eelgrass beds in a 1990 report, with arrow gobies, topsmelt, and California halibut dominant.The effects of increased urbanization in the vicinity of the bay has modified hydrology, impaired water quality, increased sedimentation, establishment invasive vegetation and predation by non-native species, and led to a greater demand for recreational use of the bay. The two tributary streams, Tecolote and Rose creeks, carry both urban pollutants and high sediment loads into the back bay. In addition, sewer lines back

up into the back bay. Moreover, the lack of water circulation in the bay allows these pollutants to accumulate.

Numerous residential, industrial, and transportation developments continue to threaten the riparian forest of the San Diego River floodplain.

San Diego River/Famosa Slough

The San Diego River drains approximately 440 square miles. The Famosa Slough includes 26 acres of wetland habitat. The mouth of the San Diego River included an estimated 3,335 acres of wetlands. Famosa Slough itself is estimated to have been greater than 45 acres. The River is listed in 1994 as an impaired water body.

Cumulative list from several biological surveys identify 164 species of which 90 were water associated. Two pairs of breeding light-footed clapper rails were documented in 1995. Fish diversity is characterized as relatively low. Special status species found at the slough include the common loon, western grebe, American white pelican, California Brown Pelican, double-crested cormorant, western least bittern, reddish egret, osprey, northern harrier, Cooper’s hawk, merlin, American peregrine falcon, Prairie falcon, West snowy plover, elegant tern, California least tern, black skimmer, loggerhead shrike, Belding’s Savannah sparrow, large-billed Savannah sparrow, and tricolored blackbird.

In addition to problems of increased urbanization and water quality concerns described for Mission Bay, Famosa Slough is affected by undirected human use, suboptimal and uncertain connection to tidal influence, and flood control concerns.

The Greater San Diego Bay Watershed

The San Diego Bay constitutes the largest estuary along the San Diego coastline, and has been extensively developed as a port. Akin to other major bays of the region, ninety percent of the original salt marshes and 50% of the original mudflats have been filled or dredged for port and urban development.

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. The San Diego Bay covers 10,532 acres of water and 4,419 acres of tidelands. There are 277,129 acres of coastal watersheds that directly are linked to the Bay. The watershed includes the Sweetwater River and Otay River drain-ages, small urban creeks (such as the Chollas) and stormwater drains flowing directly into the Bay, and portions of Silver Strand and Point Loma.The character of the mudflat and salt marsh habitats around the former mouth of the river have been transformed by human activities. Over geologic time, the waters of the San Diego River alternated between Mission (False) Bay and San Diego Bay. After settling for several hundred years on the delta

of San Diego Bay, the river was permanently diverted into Mission Bay in 1853- 1854. Seven intermittent stream systems and tidal influences created a shore lined with deltas, mudflats, and salt marshes before Europeans arrived to the embayment they later named San Diego. Waters of the San Diego River continued to flow over the delta to the Bay until the Derby Dike was built in 1853-1854, permanently diverting the river to Mission Bay. Dams were built on the Sweetwater and Otay Rivers affecting pattern and quantity of freshwater inflow, as well as sedimentation. The Bay is 15 miles long and varies from 0.2 to 3.6 mi (0.4 to 5.8 km) in width. It is about 17 square miles in area at mean lower low water. A sand spit, deposited by a northward-bound eddy of the coastal current on the west, separates the Bay from the sea. Historically, the sand transported in this way was laid down from deposition

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emanating from the Tijuana River. However, since the damming of the river in 1937, the sand supply has been cut off and northern beaches have undergone severe erosion. Zuniga Jetty, which runs parallel to Point Loma at the Bay’s inlet, was built to control erosion near the inlet, changing the Bay’s hydrodynamic characteristics by diverting both northward-bound sediment and currents (Wang et al. 1998). Broad lowlands extend about 1.5 miles south and east from the bay, before rising up into the coastal terrace, or mesa, that supports urban San Diego. Rugged Point Loma hooks around the north side, cutting off the ancient floodplain of the San Diego River, which throughout its evolution alternatively drained into San Diego or Mission Bays.Only 17 to 18% of the original Bay floor remains undisturbed by dredge or fill (Smith 1976).Freshwater contributions to the San Diego Bay come primarily from the Otay and Sweetwater Rivers, but also Telegraph Canyon (south of Sweetwater River Basin), Chollas (north end of Naval Depot south of NASSCO), Switzer (Tenth Ave. Marine Terminal [north end]), Paleta (7th Street Channel, south of Naval Repair Base), and Paradise (south of Paleta) Creeks, as well as some minor drainage groups. Construction of dams and extensive groundwater use in the Sweetwater and Otay drainages reduced the already ephem-eral input from those rivers by 76% (US Army Corps of Engi-neers 1973). Freshwater input is now limited to surface drainage from urban areas and intermittent flows from several rivers and creeks after storms. For about nine months of the year, the Bay receives no significant amount of fresh water. This can cause south Bay to become hypersaline, or saltier than seawater, in excess of 35% in dry seasons (Wang et al. 1998).Currently, the streams that lead to the San Diego Bay are channelized or confined to storm drains and sometimes completely missing. They include the mouths of Paleta Creek and Chollas Creek at NAVSTA, the mouth of Switzer Creek at Tenth Avenue Marine Terminal, Sweet-water Channel and the mouth of the Otay at the Salt Works, Telegraph Canyon Creek between the Otay and sweetwater, and small drainages in both north Bay and south Bay that drain directly into the Bay. Over 200 storm drain outfalls are located in San Diego Bay. Two rivers and five creeks provide natural drainages into the Bay in addition to the artificial storm drainage system. Stormwater outfalls provide some flows and nutrients to the Bay, but not with natural seasonality, timing, frequency, or content. Sedimentary organic matter is no longer provided to the system except what is available from below the dams on each stream system. How this has affected functioning of the Bay ecosystem has not been examined.Freshwater wetlands and riparian areas are supported at the entry points of fresh-water tributaries into San Diego Bay. They are nontidal. Freshwater marshes are generally contiguous with the upland side of the salt marshes and are occupied by cattails, rushes, and bulrushes. Freshwater riparian areas and wetlands adjacent to salt marshes have been severely impacted by development and reduced runoff from rivers and creeks. Upstream from the mouth of the Otay River is riparian habitat. The habitat is degraded and many of the trees are nonnative eucalyptus and California pepper tree. However, the riparian functions of providing habitat structure, shading some of the river, and buffering disturbances from nearby development are intact (US Fish and Wildlife Service 1998). An area known as the Egger-Ghio parcel (formerly the MKEG/Fenton parcel) was recently purchased by the Coastal Conservancy. This property lies between the southernmost salt ponds and Interstate 5, consists of former wetlands that were diked and drained decades ago and mostly converted to agricultural use.Freshwater inflows into San Diego Bay were first significantly altered when the San Diego River was permanently diverted into Mission Bay in 1875. The lower and

upper Otay and Sweetwater reservoirs were constructed for water storage in the late nineteenth century. These diversions have significantly altered the natural processes and general ecological health of the bay, including the fresh water flow, altered the coastal processes of the bay, such as wetlands, and nutrient loads that enter the Bay.

Sweetwater River/Marsh

The Sweetwater River empties into the southern end of the San Diego Bay. The eastern shores of the south Bay include the Sweetwater Marsh National Wildlife Refuge (SMNWR). The Sweetwater Marsh NWR is comprised of 4,224 acres of mainly coastal sage scrub, chaparral, riparian woodland, oak woodland, native grasslands, and vernal pools. It supports a rich diversity of native habitats and wildlife. The refuge comprises the Vernal Pools Unit and the Otay-Sweetwater Unit. The Sweetwater Marsh NWR has 316 acres of salt marsh and coastal uplands. The refuge includes the largest emergent wetlands area remaining in San Diego Bay. The Vernal Pools Unit of the NWR provides habitat for six federally listed endangered species (San Diego mesa mint, San Diego button celery, California Orcutt grass, Otay mesa mint, Riverside fairy shrimp, and San

Diego fairy shrimp). The endangered Del Mar manzanita, Orcutt’s spineflower, and Quino checkerspot butterfly may also occur in the upland habitats sur-rounding vernal pools. The Otay-Sweetwater Unit provides habitat for the threatened coastal California gnatcatcher, endangered least Bell’s vireo, endangered southwestern willow flycatcher, endangered Quino checkerspot butterfly, endangered arroyo south-western toad, endangered California red-legged frog, and listed species found in vernal pools.The refuge protects tidal marsh and adjacent upland habitat for more than 215 bird species. Two federally endangered species of bird (California tern and light-footed clapper rail), the State endangered Belding’s savannah sparrow, and one threatened species of bird (western snowy plover), as well as one endangered species of plant (salt marsh bird’s beak) are found here. It is the only place in the United States where yerba reuma (Frankenia palmeri), a member of the heath family common in some coastal marshes of Baja California, grows naturally.

A Habitat Conservation Plan (HCP) was prepared as 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. The plan is based on data collected during CSMP surveys conducted in 1987.

Otay River

The Otay River encompasses a 415 square mile area. Biological surveys conducted from 1993 to 1994 identified 104 species of which 95 were water-associated. Twenty-five of these were sensitive species, including 9 breed-ing. A total of 522,553 birds were counted. Special status species include Salt marsh bird’s beak, variegated dudleya, coast barrel cactus, California gull, California least tern, elegant tern, black tern, gull-billed tern, west snowy plover, long-billed curlew, light-footed clapper rail, black skimmer, reddish egret, common loon, western grebe, Clark’s grebe, double-crested cormorant, California brown pelican, osprey, peregrine falcon, northern harrier, Belding’s Savannah sparrow, large-billed Savannah sparrow, California horned lark, sharp-shinned hawk, Cooper’s hawk, merlin, burrowing owl, short-eared owl, and Hammond two-striped garter snake. There are several threats to the watershed, including continued modification of water quality by power plant intake and discharge; increased demand for commerce, recre-ation, waterfront development in the Bay; and continued urbanization of surrounding

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watersheds (a 1994 resources report listed 26 proposed/approved developments in the Otay Valley). There is no watershed plan for the entire San Diego Bay. The San Diego Bay Integrated Natural Resources Management Plan (US Navy 2000) was completed to address priority management actions for the Bay. 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 acres of the Sweetwater and Otay River watersheds.

Tijuana River/Estuary

The Tijuana River watershed encompasses 1700 square miles (1245 in Mexico and 455 in the US). There are 3 dams in the watershed controlling 78% of the area: Morena was built in 1912 and Barrett in 1922; in Mexico, Rodriguez was built in 1936. The river mouth once included 1,780 acres of wetland. Today, approximately 955 wetland habitat acres (intertidal saltmarsh, sand/mudflats, tidal channels and ponds) exist in this coastal watershed along the border.

The estuary is one of the largest and most studied wetlands in the South Coast, and is part of the National Estuarine Research Reserve and National Wildlife Refuge programs.

Unlike many of the sub-region’s wetlands, the Tijuana Estuary is not dissected by highways and railroads. However, since 1852, the estuary has lost 80% of its tidal prism (California Coastal Conservancy 1989). The river has received untreated sewage for extended periods intermittently since the 1930’s. The estuary has been significantly affected by sedimentation from watershed erosion, agricultural reclamation, destruction of sand dunes along the estuary’s seaward edge, urbanization, and water quality problems.

Studies show that sewage flows continue to have an extensive dilution effect on the Estuary. Raw sewage has been discharged to the River and side canyons intermittently for 50+ years, making flows perennial from 1980 to 1991. A 1990 study estimated 900 pounds of lead and 290 pounds of cyanide go into the river each year. The Estuary was listed in 1994 as an impaired waterbody; the draft list for 1996 cites selected standards exceeded for coliform, pesticides, eutrophication, metals, trash and debris.

In 1988/89 biological survey, 90 species were observed (63 waterbirds, 9 raptors, 18 upland species). Nine species of special concern were identified, including 61 pairs of light-footed clapper rail, 5 active snowy plover nests, and 303 pairs of Belding’s Savannah sparrow. Other special status species observed at the site include Salt marsh bird’s beak, salt marsh wandering skipper, California brown pelican, California least tern, American peregrine falcon, reddish egret, long-billed curlew, large-billed Savannah sparrow; and globose dune beetle on dunes. There are a range of threats to the watershed and associated wetland complex, includ-ing the presence raw sewage, sewer flows and associated effects of contamination and modified freshwater inputs; the cumulative effect of dams; sedimentation; and flood control concerns.

A phased tidal restoration program prepared in 1991 includes restoration of approxi-mately 495 acres of tidal wetlands and riparian habitat, and tidal channel improve-ments. Parts of a phased project to provide secondary treatment and an ocean outfall for raw sewage are at various stages - one is under construction, another is in

environmental review. A bi-national GIS mapping project for the watershed was begun in 1994, with the goal of developing basin-wide policies on resource management; data could be incorporated into a complementary effort to gain biosphere reserve status for the watershed, the long-term goal of which is a management plan for the entire watershed.

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