The Bon Secour NWR contains 7,000 acres of wildlife habitat for migratory birds, nesting sea turtles and the endangered Alabama beach mouse. The refuge was established by Congress in 1980 to preserve the coastal dune ecosystem, to protect threatened and endangered species, to provide compatible recreational opportunities, and to serve as a living laboratory for students and scientists. The refuge is small, compared to most national wildlife refuges, and is comprised of five separate units in Baldwin and Mobile counties, Alabama. The full-time staff consists of three, but the refuge has numerous committed volunteers throughout the year. The refuge hosts more than 100,000 visitors annually.

The Refuge is home to the endangered Alabama beach mouse, which is associated with the sand dunes and sea oats. Refuge beaches serve as nesting sites for loggerhead, and Kemp's Ridley sea turtles. Habitats include beaches and sand dunes, scrub forest, fresh and saltwater marshes, fresh water swamps, and uplands.

More than 370 species of birds have been identified on the refuge during migratory seasons. The largest are usually ospreys and several species of herons. At the other extreme, seven species of hummingbirds have been identified. Mammals such as red fox, coyotes, and armadillos are also present.

The name Bon Secour comes from the French meaning "safe harbor," very appropriate considering the sanctuary for native flora and fauna that the refuge provides. The refuge serves the additional benefit of comprising one of the largest undeveloped parcels of land on the Alabama coast. Its dunes are a reminder of the Gulf Coast, as it once existed. As a consequence, the refuge has been named as one of the 10 natural wonders of Alabama.