Pelican Island National Wildlife Refuge is located within the Indian River Lagoon, the most biologically diverse estuary in the United States. The refuge lies in a zone of overlap between the temperate Carolinian zone and the subtropical Caribbean zone, thus the flora and fauna include both temperate and subtropical species. This results in an ecosystem with diverse habitats including seagrass beds, oyster bars, mangrove islands, salt marsh, and maritime hammocks.
Some of the most extensive sea grass beds of the Lagoon are found within the refuge, including manatee grass, turtle grass, shoal grass and the threatened Johnson's sea grass, found nowhere else in the world. These sea grass communities provide spawning, nursery, and foraging habitat for many aquatic species, including spotted sea trout, redfish (red drum), snook, tarpon, mullet, sheepshead, pompano, seahorses, blue crabs, hermit crabs, pink shrimp, scallops, clams, marine worms, marine snails, and other crustaceans. Manatees and juvenile sea turtles are commonly found foraging in these areas.
Oyster bars, made up of the filter-feeding mollusks, help cleanse the estuary and stabilize shorelines. They also provide habitat for other species of mollusks, crustaceans, which support some shorebirds and waterfowl.
Salt marshes with the associated tidal creeks and mud flats consist of such marsh plants as smooth cordgrass, saltgrass, saltwort and glasswort. Salt marshes also provide abundant food and cover for a wide variety of resident and transient wildlife, including fiddler crabs, marsh rabbits, many wading birds, and shorebirds.
The mangrove habitat includes three true species of mangroves that play a vital role in the food chain of the Indian River Lagoon and also in the growth and development of many aquatic organisms. Microorganisms, which feed on decaying mangrove leaves, become food for shrimp, crabs, snails, and worms. They in turn become food for many species of fish, which support numerous wading birds in the refuge.
Mangrove trees contain several different communities of life from their roots to their canopy. The distinctive roots of the mangroves provide habitat for oysters and barnacles and sheltering habitat for many species of juvenile fish. The trunk and branches of the tree provide habitat for periwinkle snails, mangrove crabs, and mangrove snakes. The tree canopies provide nesting habitat for many species of birds.
Each mangrove species have unique adaptations to survive in the harsh saltwater environment. Red mangroves are most common along the shorelines and basins. They have prop roots that help provide oxygen, exclude salt and provide a stable foundation. Their distinctive cigar-shaped propagules are actually seeds that have already germinated before hitting the ground.
The black mangroves, predominant on natural islands (including Pelican Island) just above the tide line, have a lateral root system with pneumatophores that thrust above the ground, giving the appearance of standing on a bed of spikes. They excrete salt through the underside of their leaves. The white mangrove is found further ashore and excretes salt through pores at the base of their leaves.
Hammocks are dense stands of hardwood trees that grow on natural rises of only a few inches. Maritime hammocks are found on barrier islands near coastal strand. Maritime hammocks in the Refuge generally consist of a canopy mixture of live oaks, red bays, cabbage palms, gumbo limbos, mastic, graytwig, red mulberry, and strangler figs, with an understory of nakedwood, wild coffee, beauty berry, coral bean, laurel cherry, and marlberry. These forests support populations of wood rats, cotton mice, short-tailed shrews, bobcats, opossums, raccoons, gray squirrels, spotted skunks, great-horned owls and migratory songbirds.
Hydric and mesic hammocks are generally found at lower elevations where they are occasionally inundated with fresh or brackish water. In the Refuge these typically contain cabbage palms, wax myrtles, myrsine, palmettos, royal ferns and leather ferns. They provide habitat for land crabs, green anoles, and migratory songbirds.