Between San Diego and Los Angeles there are a series of natural lagoons where creeks flow into the Pacific Ocean. Each lagoon originally supported freshwater marsh, salt marsh, coastal sage scrub, and riparian woodland. These estuaries are linked by foraging and dispersing waterbirds during the breeding, migration, and wintering seasons. The largest of these lagoons, the Santa Margarita River mouth, is treated in the Camp Pendleton IBA. Others include:

The San Luis Rey River Estuary (Private, 200 acres) consists of riparian woodland and wetland (freshwater and saltmarsh).
Buena Vista Lagoon (DFG, >200 acres) lacks an outlet to the sea and is rimmed with freshwater marsh vegetation. There is an Audubon Center on the west end of the lagoon.
Agua Hedionda Lagoon (San Diego Gas and Electric, DFG) has about 330 acres of wetland habitat (186 acres of which is an Ecological Reserve) which are off-limits to motorized craft.
Batiquitos Lagoon (City of Carlsbad, 600 acres) is developed on all but the southern border, which features coastal sage scrub on steep slopes. In the mid-1990's, the silt dam at the mouth of Batiquitos was removed as part of a large restoration project, which also involved the construction of islands for breeding terns.
San Elijo Lagoon (DFG; San Diego Co. Parks; Non-profit, 1000 acres) contains salt marsh and mudflat, with smaller areas of freshwater marsh, riparian scrub, and, on the south side, coastal sage scrub and maritime chaparral.
San Dieguito Lagoon (DFG; San Dieguito River Park JPA; San Diego Co.; City of San Diego; Private, 260 acres) supports wetlands and agricultural lands and the majority of the valley is still largely natural.
Los Penasquitos Lagoon (CA State Parks; Private; Non-profit, 385 acres), within the City of San Diego, supports wetlands, including alkali flat habitat, freshwater marsh and riparian scrub. The slopes support lush coastal sage scrub, maritime chaparral and Torrey Pines, within Torrey Pines State Park.

Ornithological Summary

All of the lagoons support large numbers of wintering waterfowl (tens of thousands) and waders during migration and winter. Those with exposed mudflat habitat (Batiquitos, San Elijo, San Dieguito, and Los Penasquitos lagoons) provide important shorebird foraging habitat during migration and winter, exceeding 5000 individuals on single-day counts (Page and Shuford 2000). These three also feature the most extensive open land, and predictably support most of the sensitive species within this IBA. The saltmarsh habitat at Los Penasquitos Lagoon supports about 150 pairs of Belding's Savannah Sparrow (the second-largest in San Diego Co., after Tijuana Slough) and 2 pairs of Light-footed Clapper Rail (1997), while that at San Elijo Lagoon supports 40 pairs of Belding's Savannah Sparrow and 4 pairs of Light-footed Clapper Rail (1998) (Dept. Fish and Game 2000). The northernmost lagoons, Buena Vista, Agua Hedionda and Batiquitos, have more limited saltmarsh habitat, with small resident populations of Belding's Savannah Sparrows (e.g. 30 pr. at Batiquitos), and a somewhat reduced freshwater marsh avifauna that includes nesting Least Bittern, Marsh Wren (southwestern California's endemic race clarkae) and several species of breeding waterfowl (including Gadwall and Redhead)

Species dependent upon the sandy or alkali flats of the wetlands continue to be a notable feature of this IBA, especially at Batiquitos Lagoon, which supports nesting Forster's Tern, Least Tern (c. 300 pr.) Black Skimmer (30 pr.), and Snowy Plover (16 pr.) (all 1997). San Elijo Lagoon also supports breeding terns and plovers: Least Tern (20 pr.), Snowy Plover (10 pr.) (1998); Least Tern also breeds at San Dieguito Lagoon. Both Least Tern and Snowy Plover formerly bred at Los Penasquitos (until c. 1980), and may do so again given careful habitat management.

Coastal scrub habitat is most extensive at San Elijo Lagoon, which holds 20 pr. of California Gnatcatcher. Batiquitos and Los Penasquitos Lagoon have remnant populations (< 10 pr.) of California Gnatcatcher, but Cactus Wren and other scrub species have been widely extirpated from this IBA, as have sensitive riparian bird species. Currently, the San Luis Rey River mouth and San Elijo Lagoon support the bulk of riparian species within this IBA, with Least Bell's Vireo and Yellow-breasted Chat breeding at the former and Yellow-breasted Chat (2-5 pr.) at the latter [CERES (California Environmental Resources Evaluation System) XX].

Help us learn more about the birds at this IBA! Enter your birding data online at Calfornia eBird! (

Conservation Issues

The primary threats to the avifauna of these lagoons has been the sealing-off of the tidal outlets and the concurrent encroachment of urbanization. Exotic plant and animal species continue to pose a serious threat, including Red Fox. The restoration at Batiquitos Lagoon, which involved opening the tidal outlet and re-vegetating the native plant communities, should serve as an example of the possibilities for restoration within this IBA.


? San Luis Rey River Estuary (Private)
? Buena Vista Lagoon (DFG)
? Agua Hedionda Lagoon (San Diego Gas and Electric, DFG)
? Batiquitos Lagoon (City of Carlsbad)
? San Elijo Lagoon (DFG; San Diego Co. Parks; Non-profit)
? San Dieguito Lagoon (DFG; San Dieguito River Park JPA; San Diego Co.; City of San Diego;
? Los Penasquitos Lagoon (California State Parks; Private; Non-profit)


Each lagoon has a slightly different geological setting which makes them unique and and some still contain more natural habitat than others. The degree and type of marsh varies depending on whether access to tidal flushing has been restricted or not. Habitat types typically surrounding the lagoons include salt marsh and mudflat, freshwater marsh, coastal sage scrub, riparian scrub, maritime chapparal, alkali flat habitat. Some lagunes are also bordered by agricultural lands and others include areas of development.

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