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The lagoon is described as usually being cut off from the ocean by a barrier beach that forms at the mouth of the Creek. The berm is typically breached by heavy winter rains and may remain open for several months. The San Mateo Creek mouth is not listed as an impaired water body.

In biological surveys conducted in 1986, 150 species were observed of which 67 were water-associated. Seven species were special status, including the Brown pelican, double-crested cormorant, snowy plover, California gull, elegant tern, least tern, and tricolored blackbird. Five additional upland species of special status were identified. Inventories taken during the early 1990s found the following fishes: green sunfish, mosquitofish, staghorn sculpin, California killifish, and tidewater goby. Other species identified included San Diego horned lizard, and Southwestern pond turtle.

Los Flores Creek/Lagoon

The watershed encompasses 26.6 square miles, and is within Camp Pendleton. The lagoon includes 10 acres of habitat while the freshwater marsh comprises 60 acres of habitat. The lagoon and associated marsh are within a “Special Management Zone” at Camp Pendleton. Marine Corps training activities are planned to be compatible with maintaining watershed integrity. Most military activities are excluded from the lagoon and riparian area. Adjacent areas are primarily undeveloped. There are sewage treatment ponds about 1.5 meters upstream.

The lagoon is described as usually cut off from the ocean.

Camp Pendleton biologist indicate that with the exception of Belding’s Savannah sparrow and light-footed clapper rail, birds found at Santa Margarita Estuary can also be found at Las Flores (including the Western snowy plover, California least tern). In biological surveys in 1993, Tidewater goby, mosquitofish, staghorn sculpin and striped mullet were identi-fied. Camp Pendleton biologists indicate that mammal use was similar to that described for the Santa Margarita Estuary (predators observed there in 1981 included raccoon, coyote, gray fox and longtail weasel).

Of 8 coastal lagoons and estuaries sampled in 1993 at Camp Pendleton, Las Flores was described as the least affected by human impacts and the only site to have continuously sup-ported large populations of Tidewater gobies for nearly 20 years. Population data on sensitive species at Camp Pendleton is updated frequently.

Threats to the tidewater goby and other aquatic species are the presence of exotic fish species, contaminant inputs from poor sewage management practices, and other pollution from upstream.

Santa Margarita River/Estuary

The watershed is drained largely by the Santa Margarita River, Murrieta Creek and Temecula River. It is the least disturbed river system south of the Santa Ynez River in Santa Barbara County, and contains some of the largest remaining populations of several bird species, including the Least Bell’s vireo and the largest concentration of least terns in the world (State Coastal Conservancy 1989). Twenty-seven miles of free-flowing river exist on this important remnant of the South Coast wetlands. Unlike most of the rivers of the South Coast, the riparian habitat is of particularly high quality.

The coastal lagoon lies within the Camp Pendleton Naval Reservation. The slough at the mouth of the river is normally closed from the ocean by a sandbar. There are

approximately 192 wetland acres out of a historic 839 acres. The wetland complex includes salt marsh, brackish marsh, salt flats, mudflat and open water.

The floodplain was cultivated prior to 1942. Secondarily treated sewage effluent was released into the estuary from the 1940’s through the early 1970’s. Until 1970, salt flats

were used for tank training exercises. Camp Pendleton Marine Corps Base uses the area to the north, east, and northwest of the estuary for military training. Areas to the north of the estuary are leased for agriculture.

The ocean inlet is not constricted by man-made structures, but inland from the mouth, tidal influence is constrained by rock jetties from I-5 and the railroad crossings. The inlet may be open or closed for extended periods depending on rainfall and flows.

Santa Margarita River Flows vary seasonally. It is the longest free flowing river south of Point Conception in coastal southern California. The channel is braided and supports the most extensive riparian corridor in the county.

Lake O’Neill is out of the River channel but receives much of its water from seasonal river diversions. Two dams are located in the upper watershed along the two streams that join to form the Santa Margarita River. The river is included in the list of impaired water bodies.

In a 1988 report, 207 species of birds were identified, of which 85 are associated with open water, salt marsh or mudflats. Monitoring studies of aquatic life in the estuary in 1987 found 16 species of invertebrates. In 1993, fish surveys identified 22 species including 14 native estuarine and

marine species caught in the lagoon, such as California killifish, deepbody anchovy, topsmelt, bay pipefish, staghorn sculpin, and striped mullet. In the early 1990s, surveys found 18 sensitive wetland species along the lower river and estuary, including 3 breeding sites for endangered birds (486 nests of California least terns, 120 pairs of Belding’s Savannah sparrow, and 34 nests of western snowy plover).

Threats to the wetland complex include invasive species, land-use development in the upper watershed, and the potential for modifying river hydrology and increased sedimentation associated with land development.

Various sensitive lands in the watershed have been preserved as open space and as an ecological reserve by both private and public landowners. Working with the US Fish and Wildlife Service, the Marine Corps has developed an ecosystem management plan to ensure that Base training activities are compatible with endangered species habitat needs. Numerous studies and management projects include a cooperative effort among San Diego and Riverside counties, and federal and state agencies and community groups to develop a watershed plan focusing on land uses, such as flood control, erosion, sedimentation and the long-term effects of urbanization on the river’s habitats; other enhancement and education efforts are also underway in sub-watersheds.

The Watershed Enhancement Plan (California Coastal Conservancy 1995) details the purpose and goal of the Santa Margarita Watershed Enhancement Plan and outlines the scope of work for the project.

San Luis Rey River/Estuary

The watershed encompasses 565 square miles. The San Luis Rey River Estuary is located in the City of Oceanside. The watershed extends into unincorporated San Diego County. There are 164 wetland acres out of a historic 2,200 acres of high marsh and 58 acres of low marsh (as indicated by the 1893 USGS map for the lower portion of the river).

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Henshaw Dam, built in 1922, controls 36% of the watershed, and three small reser-voirs. The mouth of the San Luis Rey River is not listed as an impaired water body.

Biological inventories in 1995 reported several sensitive species in riparian and wetland areas of the lower river. Special Status Species identified in the report included osprey, black-shouldered kite, white-faced ibis, western least bittern, western snowy plover, Belding’s Savannah sparrow, least Bell’s vireo, tricolored blackbird and the southwestern pond turtle. The primary wildlife values of the river are associated with riparian habitat and the small marsh at the river mouth. Brown pelicans and least terns feed and roost in the lagoon.

Agriculture and urban development (and associated flood con-trol activities) within the floodplain and watershed continue to threaten habitat and aquatic species. A Habitat Conservation Plan was developed for the river’s least Bell’s vireo population and is currently being implemented. The plan designates 12 acres of riparian habitat west of I-5 as Conserved Habitat.

The San Luis Rey River Resources Report was prepared to provide a base of information for the development of the San Luis Rey River Watershed Comprehensive Plan.

Buena Vista Creek/Lagoon

The watershed encompasses 19 square miles. Buena Vista Lagoon provides one of the only freshwater wetland habitats on the South Coast. Numerous migratory waterfowl visit the lagoon each year. The lagoon lies within the cities of Carlsbad and Oceanside in northern San Diego County. There are 223 acres of wetland out of a historic 666 acres.

Biological inventories in 1994 identified 103 species of which 56 were water-associated and 47 upland species. The inventory identified 6 raptors, and 8 water-associated sensi-tive species, including California Least tern, Belding’s savannah sparrow, and a single light-footed clapper rail. Special status species identified include American white and California brown pelicans, double-crested cormorant, light-footed clapper rail, California gull, California least tern, loggerhead shrike, Osprey, Northern harrier, Cooper’s hawk, and Western spadefoot.

Urban development surrounds the lagoon. Circulation and flushing are constrained by roadfills for I-5 and other developments. Developments surrounding the lagoon and on the creek flood plain continue to threaten the wetland. The lagoon suffers from extreme sedimentation due to the effects of urbanization in the watershed. A number of other threats to watershed are erosion and sedimentation in the watershed, and the introduction of exotic plant and animal species.

In 1983, the Conservancy began working with local cities to lower peak flows and reduce erosion in the creek and sedimentation of the lagoon. In 1983, 160,00 cubic yards of sediment were dredged from the east basin and 2 least tern nesting islands were created.

Agua Hedionda Creek/Lagoon

The watershed encompasses 29 square miles. The lagoon covers 330 wetland acres (200 acres are privately owned). In 1954, the lagoon was completely dredged to provide a deep basin and source of cooling water for the Encinas power plant. The lagoon is located within the City of Carlsbad off Carlsbad Boulevard.

The southern shore of the outer and middle lagoons is occupied by a power plant and support facilities. Agricultural activities occur to the south and residential development is located to the north. The southern shore of the inner lagoon is undeveloped with adjacent land used for agriculture. Carlsbad Blvd. and the ocean are located to the west of the lagoon. The area to the east of the inner lagoon is undeveloped. Sedimentation from agriculture and urban development in the watershed, pressure on habitats and wildlife from active recreation and adjacent development, and impacts to water circulation from the power plant.

The original slough was only occasionally open to the sea. An inlet channel of rip rap jetties, which keeps the mouth permanently open, was built in 1954. The power plant draws water from the lagoon and discharges the cooling water into a second discharge channel that empties directly into the ocean. The three basins of the lagoon are connected via openings under I-5 and the railroad. However, the berms for these crossings limit the reach of tidal action. The watershed is included in 1996 draft list of impaired water bodies; selected standards exceeded for sediment and coliform bacteria.

Biological surveys taken during 1994 to 1995 found 81 species; 61 water associated and 20 upland species. Twelve sensitive wetland species were observed, including nesting Belding’s Savannah sparrow, California least tern, western snowy plover, brown pelican, white-faced ibis, California gull, osprey, cooper’s hawk, long billed curlew, log-gerhead shrike, northern harrier, and black skimmer. Twenty-nine species of fishes were collected at 21 stations throughout the lagoon, including Silversides, gobies, diamond turbot, among others. A number of marine fish species also inhabit the lagoon.

San Marcos Creek/Batiquitos Lagoon

The watershed encompasses 52 square miles, and is located between the Cities of Leucadia and Carlsbad, at the southern edge of Carlsbad. San Marcos Dam, constructed in 1952, controls approximately 53% of the watershed. There are 542 acres of (pre-enhancement) wetlands. It is estimated that the historical amount of wetland habitat exceeded 700 acres. In 1983, the lagoon was made a DFG State Ecological Reserve. Passive recreation is the predominant use.

In biological inventories taken during 1994, 136 species were observed of which 76 were water-associated species, including 14 sensitive (8 additional sensitive species were found in other habitats). Sensitive species observed include Common loon, American white and California brown pelican, double-crested cormorant, white-faced ibis, osprey, light-footed clapper rail, western snowy plover, long-billed curlew, California gull, caspian tern, elegant tern, California least tern, black skimmer, long billed curlew, white-faced ibis, Belding’s Savannah sparrow, osprey, and 8 additional upland species. Both the California least tern and Belding’s Savannah sparrow were nesting in the area. Western snowy plover were also observed. A total of 6 species of fish were caught at three stations, including Mosquitofish, California killifish, mudsucker, pipefish, bluegill, and small mouth bass.

The major threats to the lagoon are sedimentation, eutrophication, and recre-ation impacts from agriculture and urban development in the watershed. If current sedimentation rates continue, the entire lagoon could be filled in 40 years (California Coastal Conservancy 1989).

There is no watershed management plan for the area. In 1984 the Coastal Conservancy prepared the Batiquitos lagoon enhancement plan. To mitigate impacts at the Port of Los Angeles, the Port is currently implementing the Batiquitos Lagoon Enhancement Project, which was developed cooperatively with resource agencies and includes some recommendations from the Conservancy plan. The project involves dredging the lagoon, constructing new inlet jetties to keep the mouth open and permanently restoring tidal flows, and creating nesting areas for colonial nesting birds

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including the California least tern and western snowy plover. The project includes 10 years of monitoring for biota and water quality. In 1987, the Coastal Conservancy prepared the Batiquitos lagoon watershed sediment control plan. This plan recommended construction of sediment traps and was not implemented. In 1989, the City of Carlsbad and the Port of LA completed a sediment load study for the lagoon, which concluded that inadequate tidal flushing was a greater factor in the rapid filling of the lagoon than sedimentation from upland sources.

Escondido Creek/San Elijo Lagoon

The watershed encompasses 77 square miles and includes the major tributaries of Escondido and La Orilla creeks. The lagoon includes 530 acres of primarily shallow-water brackish wetland that rarely experiences tidal flows. Like several other wetlands of this subregion, this lagoon is important habitat for small fish, invertebrates, aquatic insects, and migratory shorebirds and waterfowl. The area is designated as an Ecologi-cal reserve/open space/parks in the Encinitas General Plan.

The lagoon was once a fully tidal system. Several dikes and levees were constructed between 1880 and 1940 to create access roads, duck ponds, and sewage treatment ponds. The dikes have eroded and hunting was discontinued in 1971. From 1940 until as late as 1973, the lagoon received wastewater from the City of Escondido. Today, Highway 101, the railroad, I-5, and the east basin flood control dike limit the reach of tidal action. The lagoon is connected to the ocean via a narrow rip-rapped channel. The tidal prism is insufficient to maintain an open ocean inlet.

Biological surveys conducted in 1994 identified 130 species of which 76 were water-associated, including 13 sensitive species (and 10 sensitive upland species). Sensitive species include the light-footed clapper rail, California least tern, western snowy plover, Belding’s Savannah sparrow nesting, San Diego marsh elder, Common loon, American white and California brown pelicans, double-crested cormorant, white-faced ibis, long-billed curlew, elegant tern, North harrier, sharp-shinned hawk, Cooper’s hawk, Osprey, and 12 other sensitive bird species nesting in upland areas, including the California gnat-catcher and the Salt Marsh wandering skipper.

The major threats to the lagoon include fluctuating salinity levels, eutrophication, high levels of bacteria, accelerated sedi-mentation, and excess freshwater. The lagoon was listed in 1994 as an impaired water body. The draft 1996 list indicates selected criteria for eutrophication, sediment and coliforma bacteria were exceeded. Other problems are associated with agriculture and urban development in watersheds, including exotic vegetation and fauna, off-road vehicle activity, and increased visitor usage also affect wildlife.

San Dieguito River/Lagoon

The San Dieguito Lagoon was the largest of the subregion’s coastal lagoons and has the largest watershed. It is also the only lagoon of the subregion in which most of the land is not publicly owned. Therefore the lagoon and river channel are constantly being threatened with development. The watershed encompasses 345 square miles, 302 of which are behind dams. Lake Hodges, completed in 1919 and Lake Sutherland completed in 1954, are the two major dams that block the river. Three tributaries join the San Dieguito River below the dam while 2 other small drainages empty directly into the lagoon basin. The lagoon includes 260 approximate wetland acres. Before 1880, the marsh area is believed to have been over 600 acres, with the entire lagoon covering 1,000 acres.

San Dieguito River Flow is intermittent and the river bed upstream of tidal influence is often dry. The channel is substantially unarmored except for a concrete block revetment along the upper bank from approximately Jimmy Durante Blvd to the ocean.

Tidal salt marsh has survived along the river channel and in the tidal basin, and non-tidal pickleweed marsh exists in several areas of the eastern lagoon. Tidal mudflats cover the river channel and tidal basin margins. There is also riparian habitat in the lagoon, as well as considerable filled area that could be restored to tidal marsh.

In biological surveys conducted during 1992 to 1993, 143 species were identified, including 15 sensitive and 9 invasive. Fifty-two percent of the species were water birds, including the breeding Belding’s Savannah sparrows and ten pairs of California least tern. A number of fish were identified in 1994 surveys, including 14 special status species, including yellowfin goby and mosquitofish. Spe-cial species identified include San Diego horned lizard, orange-throated whiptail, common loon, brown pelican, white-faced ibis, osprey, north harrier, sharp-shinned hawk, West snowy plover, long-billed curlew, California gull, elegant tern, California least tern, black skimmer, tricolored blackbird, Belding’s Savannah sparrow, and Cali-fornia gnatcatcher.

The major threats to the watershed are continued development and urbanization. There are also structural constraints on the reach of tidal flow that is needed by birds and fishes, problems with exotic vegetation, flood control concerns, retention of freshwater flows, and the presence of sand and gravel behind dams.

In 1994, the San Dieguito River Park Joint Powers Authority prepared a conceptual plan for a regional open space park for 55 miles of the river corridor with the goal of preserving and restoring land to protect natural, cultural resources, and provide compatible recreation (1/3 of the land within the planning area is publicly owned). The City of San Diego drafted the San Pasqual Valley Plan [completed in 1994] to resolve issues regarding endangered species habitat, flood control, mining, agriculture, and water quality in the valley.

Los Penasquitos Lagoon

The watershed encompasses 95 square miles, and is located in the City of San Diego. The tributaries of the watershed, Los Penasquitos Creek and Carmel Creek, flow year-round due to development in the watershed. Approximately 3650 acres of Los Penasquitos and Lopez canyons are in the Los Penasquitos Canyon Preserve. The goals for the Preserve are preservation and enhancement of natural and cultural resources. There are approximately 440 acres of wetland habitat out of a historic 630 acres. The Conservancy owns a 20-acre area of the upper portion of the lagoon, near the outlet of the Creek.

An active management program is targeted towards keeping the mouth open. When the mouth is open, the tidal reach is impeded by the railroad and sewer berms.

Biological inventories in 1994 found 183 species of which 64 were water-associated species, including breeding Belding’s Savannah sparrows (156 pairs) and one pair of light-footed clapper rails. Special status species include Salt marsh daisy, common loon, western grebe, brown pelican, white-faced ibis, western snowy plover, long-billed curlew, California gull, elegant tern, California gnatcatcher, Cooper’s hawk, and peregrine falcon.The lagoon suffers from sedimentation and lack of tidal flow. The lagoon, like most lagoons of the subregion, is filling in. Erosion and sedimentation problems are common problems facing the lagoons of the subregion, including Los Penasquitos. This lagoon

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