Once a shallow pool closed to the Pacific at low tide, the lagoon was dredged and opened to a continuous tidal flow to cool an electrical power plant, the Encina Power Station, constructed in 1954. The expanded lagoon became home to blue herons, brown pelicans, ibises, snowy egrets, western grebes, double crested cormorants, black-crowned night heron and forty-seven other species of birds, as well as 27 species of mammals, 4 species of amphibians, 5 species of lizards and 8 species of snakes, along with a multitude of aquatic life. Frequent visitors to the lagoon also include dolphins, seals, sea lions and sea turtles.
Agua Hedionda Lagoon forms a part of the complex of coastal wetlands which are an integral part of the Pacific Flyway, the migration route that myriads of water birds, shorebirds and other water-associated birds follow from their breeding grounds in the north to their southern wintering grounds. Agua Hedionda Lagoon’s singular features of significance to birds is the ocean connection which produces extensive tidal flushing, its relatively deep water with steep slopes at the margins, rock banked in several portions, areas of mudflats, salt marshes and intermittent vernal, freshwater marshland. Fifty-five species of water-associated birds were identified during occasional observations. Fall-winter influxes of Pacific Flyway migrants produce population highs which are succeeded by spring-summer population lows, when small numbers of “summering” migrants and a modest number of nesting resident species remain after the northward return passage of most migratory birds.
Agua Hedionda Lagoon attracts moderate numbers of water-birds, divided almost equally between wading varieties and swimming-diving forms. The most common of the birds drawn to the deeper waters are the scaup. Shorebirds and ducks are among the most common of the water-associated birds attracted to the lagoon, including bufflehead, surf scoter and ruddy ducks, the red-breasted merganser, the horned, eared and western grebes, the California, western, ringbilled, Bonaparte’s and Heermann’ s gulls, the Forster’ s and Caspian terns, double-crested cormorant; and the common coot. Portions of the shoreline, mudflats and marshy sites, particularly at the eastern end of the lagoon, attract shorebirds in moderate numbers and wading birds in small numbers. The most abundant of the shorebirds observed at the lagoon are the snowy plover, killdeer, black-bellied plover, dunlin, dowitchers, godwits, sanderlings and sandpipers. The great blue heron, green heron and black-crowned night herons are the large wading birds seen in the area, but only in small numbers. Several species designated “endangered” or “rare’” occur at Agua Hedionda Lagoon. The California least tern, classified as an endangered species by the U.S. Fish and Wildlife Service and the State of California Department of Fish and Wildlife, regularly nests on the sand flats at the east end of the lagoon. California brown pelicans roost each night on the ball and barrel floats of the Carlsbad Aquafarm, making the site, one of the largest roosting sites of the brown pelican on the West Coast.
The endangered Belding’s savannah sparrow breeds in the salt marshes of Agua Hedionda Lagoon; a census of this small sparrow that virtually depends upon pickleweed marsh for its existence, recorded 37 singing males. Forty seven different species of land birds have been observed along the shores of lagoon’s upper basin where a mixture of grasslands, coastal sage scrub, salt marsh and freshwater marsh provide an ideal habitat for 8 species of hawks, kites, falcons and owls, two species of game birds, mourning dove and the California quail, 5 species of humming birds, 1 species of woodpecker, the common flicker, the kingfisher and 29 species of passerine birds, including 25 species of songbirds, including the yellow warbler.
The upland habitats surrounding Agua Hedionda Lagoon support a diversity of 27 native mammal species, ranging from dusty-footed wood rat, cactus mouse and California mouse to raccoon, bobcat and coyote. The upper lagoon is feed by fresh water from Agua Hedionda Creek, creating an intermittent brackish water pond habitat and breeding site for frogs, toads, salamanders and crayfish, providing food for raccoon and coyote.