The refuge has some of the largest seabird colonies in the nation and has been identified as a Globally Important Bird Area by the American Bird Conservancy and The Nature Conservancy. Approximately five percent of the islands are used by nesting birds. These nesting colonies are most active March through August. Nesting colonies must not be entered. The refuge is open year-round, but visitors must obey posted closed areas and avoid disturbing the birds.
You can enjoy the seabird colonies from a respectful distance. From late winter through summer the islands are a raucous flurry of avian activity. Visitors typically see brown pelicans, piping plovers, royal, sandwich and Caspian terns, black skimmers, and laughing gulls. Different bird species tend to nest in various zones, with the pelicans farthest from the shore. Tern nests are often just a scrape in the sand.
The Chandeleur Islands are one of only four Gulf of Mexico wintering grounds for the redhead duck, which primarily winter where they can feed in seagrass beds. Other species of waterfowl such as bufflehead, scaup, gadwall, and blue-winged teal use the refuge as a migration stopover. Winter aerial surveys of the islands have counted thousands of ducks, primarily redheads and scaups.
Several species of shorebirds can be found at the islands, including the Wilson's plover, American oystercatcher, snowy plover, dowitchers, dunlin, sanderlings, red knots. least and western sandpipers, and the piping plover. The eastern seaboard population of piping plovers is threatened, the refuge provides critical wintering grounds for this small shorebird.