The song of the marsh wren announces the arrival of spring at the refuge.  Barn swallows, salt marsh song sparrows, and common yellowthroats dot the marsh with color, while tiny, sand-colored western snowy plovers begin nesting on the salt flats.  March through May is the best time to see wildflower displays, and to view the millions of birds that pause at the refuge during their northerly migration.

In warmer months, the refuge acts as a nursery to many different animals raising their young.  More than 80 species of birds, including the endangered California clapper rail nest on sites throughout the refuge.  Harbor seals haul out in protected sloughs to give birth to pups and nurse their young.  Native gray fox pups are often seen scampering across the upland near dusk.

The migratory frenzy begins in August with the arrival of hundreds of thousands of shorebirds making their way south from the Arctic, Alaska, and western Canada.  Twenty-five species of waterfowl follow in October, which is also one of the best times to see migratory golden-crowned sparrows and yellow-rumped warblers.

Winter at the refuge is a prime time to view both waterfowl and shorebirds along the Bay, sloughs, and marshes.  Great "rafts" of surf scoters, lesser scaups, ruddy ducks and bufflehead float along the Bay, while flocks of eared grebes drift in nearby salt ponds.  With luck, you may see a golden eagle soaring overhead, scanning for rabbits and other prey.