Approximately 140,000 shorebirds, representing 37 species use Bolivar Flats for both feeding and roosting. The federally endangered species brown pelican and peregrine falcon are other important species using the flats for roosting and feeding. The adjacent salt marsh hosts clapper rails, seaside sparrow, and sharp-tailed sparrow. Black Skimmers and Least terns attempt to nest on the flats every year, but usually are not successful because of vehicular traffic. The huge bird population is largely supported by Bolivar Flats' rich, benthic infauna.
Polychaet worms are the most abundant benthic animals.
Shorebird use is highest in the winter and in early spring. Dunlin, Western Sandpipers, Short-billed Dowitcher, and American Avocet are the most abundant winter shorebirds. Willets and Wilson's Plovers nest at the site. Willets, Black-bellied Plovers, and Sanderlings occur all year. The area is also one of the most important wintering sites for the threatened Piping Plover.