Wintering waterfowl populations on the refuge vary from 500 to 3,000 depending on the availability of water. From November through January, peak numbers of diving ducks and shorebirds, such as ruddy ducks, gadwall, and Northern pintail, can be seen on the saline pond and the Salinas River from the walking trails.

The dunes are awash with color as native shrubs and flowers are in bloom. Western snowy plovers stake out favorite spots to nest, and the spectacles known as the spring and fall migrations bring thousands of birds to the refuge. In addition to ducks and shorebirds, peregrine falcons, merlins, and ospreys can be seen along the River Loop Trail. Spring migrants like the American goldfinch and Wilson’s warbler are a common sight, and fall migrants including the yellow warbler, white-crowned sparrow, and Pacific-slope flycatcher are visible along the River Loop Trail and parts of the Beach Trail.

By April and May most of the migrant birds have flown north to nest, while residents choose to nest on the refuge. Some nesting waterbirds on the refuge include American avocet, black-necked stilt, and Caspian tern. Western snowy plovers and their young chicks can be seen on the beach, in the dunes and along the edge of the saline pond. In the upland areas along the River Loop Trail, nesting barn and cliff swallows, common yellowthroat, and song sparrows are common. Birds such as gulls, herons, and egrets can be seen year round feeding and roosting on the refuge. Some non-breeding birds that visit the refuge are brown and white pelicans. As many as 1,400 pelicans have been seen roosting at the river mouth during the summer.