Approximately 37 percent of the refuge is made up of salt marsh, brackish marsh, and freshwater marsh.  Salt marsh is one of the most productive habitats on earth and creates the foundation of many food webs  Two endangered species, the California Clapper Rail and Salt Marsh Harvest Mouse rely on tidal salt marsh for their survival.

Man-made ponds were originally constructed for the purposes of producing salt.  Plant and animal species found in a given salt pond are determined by the salinty (concentration of salt in the water).  Fish such as topsmelt, goby, and perch thrive in low to  moderately salty waters, and the endangered California Least Tern takes advantage of these fish populations for its food.  Approximately 48 percent of the refuge is comprised of salt ponds.  As part of the South Bay Salt Pond Restoration Project, most of these ponds are being restored back to tidal influence. 

Seemingly barren, mudflats are actually teeming with life. A handful of Bay mud may contain 40,000 tiny living creatures. The secret of the mudflat abundance is the two tidal cycles that occur each day. Tidal water flowing in and out of the Bay creates strong currents that distribute enormous quantities of nutrients throughout the Bay, sloughs and marshes. Fish and shorebirds feast on the abundant creatures brought in by the tide, which include zooplankton such as copepods. Mudflats make up 12 percent of the refuge. 

Vernal pool habitat is a small, but vital part of the refuge. The refuge has 700 acres of vernal pool habitat.  Vernal pools are short-lived, seasonal wetlands. Several species, such as endangered vernal pool tadpole shrimp and Contra Costa goldfields are found only in this type of wetland. Resident wildlife are well adapted to the alternating wet and dry periods, with most animals and plants taking advantage of winter and spring rains to reproduce. As the pools dry in the spring, yellow goldfields and purple downingia rim the pools with brilliant color. Some animals, such as fairy shrimp and other invertebrates remain as dormant eggs throughout the long, dry summers. Adult amphibians such as the California tiger salamander migrate to vernal pools to breed and juvenile salamanders leave the vernal pools as they dry during late spring and early summer.

Approximately 2 percent of uplands habitat make up the refuge.  Rising above the salt marsh is the drier upland habitat, where jackrabbits, fence lizards, California towhees, and gray foxes are found.  Coyote brush, oaks and a variety of grasses provide cover for these animals.