The majority of water birds which have been recorded from Los Peñasquitos Estuary are migratory waterfowl and shorebirds that rest and feed in the lagoon during their flight in fall and on their return in spring to their northern breeding grounds. The shorebirds and waders frequently may be observed probing the mudflats for worms, clams and insects at low tide or resting in the salt pan areas at high tide. Diving birds, such as cormorants, grebes and pelicans, are most commonly seen in the deeper tidal channels near the lagoon entrance. The majority of ducks usually congregate in the large ponds on the southwest side of the lagoon where the freshwater stream enters.
Relatively few birds are permanent residents of the lagoon area. However, several showy species such as the stately Great Blue Heron, and the vociferous Black necked Stilt and Killdeer are often seen. The Stilts and Killdeer nest on the dry salt pan area on the southwest side of the lagoon.
Several other birds are frequently seen in the lagoon area although they ate not dependent on the marshland for their survival. The commonest bird in the Pickleweed vegetation is the dainty, speckle breasted Savannah Sparrow. The flute like tones of the Western Meadowlark, and the guttural “kwaak” of the Black crowned Night Heron are frequently heard at the western end of the marsh and the scarlet flash of the Red winged Blackbird is a common sight among the cat-tails and wild mustard at the eastern end of the lagoon. Two fairly common predatory birds are the slender, graceful Northern Harrier and the handsome Black shouldered Kite; both may be seen gliding over the salt marsh in search of small rodents and birds. The Kites, which only a few years ago were in danger of extinction, are becoming commoner in the Reserve, and Red tail and Red shouldered Hawks, Pelicans and Ospreys are also occasional visitors.
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