The refuge provides habitat for nine species of Federally-listed threatened or endangered species and is home to 227 species of birds, including 8 percent of the world population of the western snowy plover. It protects 60 percent of the world's population of California clapper rail, as well as a substantial number of salt marsh harvest mouse, both found only in the remaining tidal marshes of San Francisco Bay.

Wintering waterfowl make extensive use of the area, averaging 45,000-75,000 each winter. More than 500,000 shorebirds make use of the mud flats and salt ponds. Globally significant numbers of at least eight species of shorebirds visit this refuge during migration.

Nearly 700,000 people visit the refuge each year, including 10,000 school children, teachers, and parents, who take part in the refuge's nationally recognized environmental education programs.

The refuge provides wildlife-oriented recreation opportunities at its Fremont Visitor Center, Alviso Environmental Education Center, over 30 miles of hiking trails, and its accessible fishing pier that extends into San Francisco Bay.

Turn right at the refuge entrance sign and follow Marshlands Road to the stop sign. Turn left into the parking lot. To environmental education center (Alviso-San Jose): From Interstate 880 or Highway 101, exit on Highway 237 toward Alviso.

Turn north on Zanker Road. Continue on Zanker, which turns into Los Esteros after a road bend, to the environmental education center entrance (a sharp right turn at Grand Boulevard), approximately 2.1 miles from Highway 237.

Predator management activities are conducted to reduce impacts of non-native predators on endangered species. Each year, refuge treats invasive non-native plants, particularly Lepidium and Spartina alterniflora, to prevent losses of native marsh species.

Biological monitoring programs are conducted for endangered species and waterfowl, including annual winter airboat surveys and spring call counts for the California clapper rail and nest surveys for snowy plovers. The refuge remains in the active land acquisition stage, with 30,000 of the 43,000 acres authorized by Congress already acquired.

As a result of agreements reached during early acquisition process, approximately 17,000 acres of the refuge consists of salt ponds managed for evaporative solar salt production by Cargill Salt Company.

These ponds are also used by shorebirds, waterfowl, herons and egrets which are attracted by the small fish, brine shrimp, and other invertebrates that live in many of the ponds, based on salinity levels. Brine shrimp are also commercially harvested on a limited basis through special use permits.