The refuge is an important resting and feeding area for migratory birds including gulls, terns, neotropical migratory songbirds, and shorebirds. Least terns, black skimmers, Wilson's plovers, and several other shorebird species have nested on the spoil deposits on Tybee. During all seasons, the refuge's shoreline and open spoil deposits are used as resting sites for brown pelicans, gulls, and terns. Endangered species, including piping plovers and wood storks, have been observed on the refuge land, while shortnose sturgeon and manatees have been found in the waters bordering Tybee. With the use of telescopes, birdwatchers observe the refuge birdlife from levees located across the river within Fort Pulaski National Monument.