From the muddy shores of the lagoon to the skies above, the reserve hosts a rich diversity of life.
The mosaic of habitats at San Elijo Lagoon Ecological Reserve supports more than:
- 23 species of fishes
- 20 species of reptiles and amphibians
- 26 species of mammals
- 300 species of birds (of which 65 have been documented to nest in the reserve).
San Elijo Lagoon is one of few remaining coastal wetlands in Southern California. In 2009, the Conservancy hosted its first Bioblitz, a 24-hour inventory of all living organisms in San Elijo Lagoon Ecological Reserve. Participating scientists confirmed more than 735 species of fishes, spiders, insects, reptiles, mammals, birds, amphibians, plants, algae, and fungi. Wildlife flourishes in this region, and its continued protection is critical to ensure that our future generations will enjoy this wetland's incredible biodiversity.
BIRDS
Bird watchers from around the world flock to San Elijo Lagoon to marvel at its avian abundance.
Bird habitation at San Elijo Lagoon has been one of the most studied biological elements of the reserve and, due to abundance, variety, and high visibility, the component most noticed by the public. More than 319 species have been recorded at San Elijo Lagoon and Cardiff State Beach. More than 106 of these species are rare to uncommon migrants, and 74 are considered sensitive, threatened, or endangered species, including 16 of the 65 nesting species. Additional migrant species potentially occur, particularly offshore.
Marsh Wren (Photo: C. Taylor)
Numbers of individual birds range into the thousands when considering migratory shorebirds and waterfowl, into the hundreds for pelicans and cormorants, coots, gulls, terns, swallows, warblers, and sparrows. Such numbers and diversity are attributable to geographic/physical factors of location, variety of habitats and ecotones, and variety and abundance of food items.
The mild climate of San Elijo Lagoon accommodates large numbers and varieties of birds. Resident species, transient migrating species en route between lower latitude wintering grounds and higher latitude breeding grounds, wintering species migrating from elsewhere, and breeding species that winter elsewhere can be found during the year. The coastal location and maritime influence on weather, varied topography and soils, estuarine influence of both fresh and salt waters create a diverse assemblage of plant types and habitats. These habitats, in turn, provide a wide variety and abundance of food items such as submerged vegetation, seeds and flowers, benthic invertebrates, fishes, aquatic and surface dwelling invertebrates, terrestrial invertebrates, amphibians, reptiles, small and large mammals, and the remains left thereof, allowing a vast array of niches to be exploited.
Urbanization of Southern California has resulted in loss of habitat and habitat degradation. Accumulation of toxins from past and current industrial and agricultural products, including continued use elsewhere of chemicals banned in the U.S., together with historic, and, in some cases, continued hunting and persecution, have produced endangered species. Several sensitive, threatened, and endangered species rely on San Elijo Lagoon Ecological Reserve. More than 105 species of concern have been documented in the reserve, including 33 of the 81 to 93 species that breed around the lagoon. The federally endangered Brown Pelican roosts and feeds regularly in the lagoon, the Light-Footed Clapper Rail is resident, and the California Least Tern nests, forages, and roosts around the lagoon each summer. Least Bell's Vireo presence has increased in recent years with nesting along Escondido Creek. The federally threatened Snowy Plover, California Gnatcatcher, and state endangered Belding's Savannah Sparrow nest and are present throughout the year. The recently delisted Peregrine Falcon is a regular visitor. Bald Eagles and Willow Flycatchers forage in the reserve occasionally. In the past, Wood Stork, Black Rail, Sandhill Crane, and Bank Swallow have been documented in the lagoon, and cactus wrens were once abundant in adjacent sage scrub.
To better document current bird use of the lagoon, monthly bird counts are conducted by volunteers of San Elijo Lagoon Conservancy.
MAMMALS
 Several families of Mule deer, named for their large mule-like twitchy ears, inhabit the eastern end of the reserve. Fortunate trail walkers may catch a glimpse. Many of the reserve's mammals live secretive lives in the dense underbrush, such as the nocturnal Dusky-Footed Wood rat, an animal that builds stick and "pack rat" nests that have been known to house generations of offspring.
Southern mule deer
The luckiest of trail visitors have glimpsed the elusive bobcat with its ear tufts and black-tipped stump tail. Coyotes, rabbits, and others are among the 26 species of mammals that reside in the reserve.
REPTILES & AMPHIBIANS
San Elijo Lagoon is a place where land and sea converge, fresh and salt water are mixed by tides, and desert winds meet coastal fog. In this rare environment, some of the smallest reptiles and amphibians have become critical indicators of the health of the lagoon.
 Alligator lizards dart from your shadows, though camouflage helps blend into rocks and dirt. Silvery legless lizards slide across sand dunes. Coast Horned Lizards not only have spikes for defense, they can eject blood from their eyes when threatened. Don't let the Gopher snake fool if it hisses or shakes its tail.
Western fence lizard (Photo: D. Ancinec)
The gopher snake can be confused with the venomous (if overtly threatened) Southern Pacific Rattlesnake, which can be gray, olive, or brown with a dark diamond pattern.
FISHES & INVERTEBRATES
Primarily a shallow-water estuary, San Elijo Lagoon is one of few remaining coastal wetlands in Southern California. The watershed that drains into the reserve covers 77-square miles and includes the surrounding beach communities. Most fresh water comes from Escondido Creek, but there are storm drains into the lagoon from coastal towns. Like rainforests and coral reefs, wetlands are one of the most endangered habitats in the world. Those that remain need our continued protection.
 Wetlands provide nursery grounds for many fishes and invertebrates, including commercially-important species, such as the California halibut.
Mullet (Photo: R. Spencer)
Shell middens, the refuse heaps of Kumeyaay, who were the last Native Americans to thrive here, show a reliance on a rich abundance of seafood found a few centuries ago, such as scallops, clams, sharks, barracuda, bonitos, and abalone. During high tides, silvery mullet leap from still waters with an astounding splash, as if to prove their resilience to low oxygen levels. At low tide, thousands of California horned snails emerge to feed on algae. The larger Striped Shore crab can grow to two inches in length and will scavenge for algae, diatoms, smaller invertebrates, and dead animals. The life cycle of wetlands continues from the largest of mammals to microscopic life submerged by incoming tides and brackish waters.
INSECTS
 Darting among marsh grasses or nearly invisible in riparian canopies, many insects call this reserve home, from beetles and butterflies, to bees, dragonflies, and many more. We adore them for their brilliance (think Lorquin's Admiral) and ability to skim over water within daring distance. Other insects scuttle across a trail, like the Darkling Beetle.
Red skimmer (Photo: J. Walker)
Birds and other animals rely on insects for food. Plants in the reserve play host to intrepid winged insects, eager to attach pollen in an effort to continue life's cycle.
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