The constant influx of nutrients from the Suwannee River combined with numerous off-shore islands and tidal creeks create excellent wildlife habitat which supports kites, bald eagles, manatees, sturgeon, deer, and turkeys, to name but a few of the species which take refuge there.

The Suwannee River and nearby bottomland hardwood swamps, pine forests, cypress domes, tidal creeks, and vast salt marshes provide habitat for thousands of creatures every year.

Many species including white-tailed deer, wild turkey, bobcat, bats, alligator, raccoon and river otter are present throughout the year — feeding, nesting, loafing, and roaming the forests and swamps.

Gulf sturgeon, Florida salt marsh vole, eastern indigo snake, gopher tortoise, and wood stork are examples of threatened or endangered species that find suitable habitat within the refuge.

Numerous birds, including the striking swallow-tailed kite, bald eagle, osprey, prothonotary warbler, and dozens of species of shorebirds use the refuge seasonally then migrate farther south during winter months.

These areas provide important foraging habitat for thousands of shorebirds, such as sandpipers, dowitchers, American oystercatcher, ruddy turnstone, and plovers, as well as diving ducks.

Under special-use permits, the University of Florida and the United States Geological Survey are involved in on-going research activities on the refuge for various species including salt marsh voles and mosquitoes.