Bon Secour National Wildlife Refuge was established by Congress in 1980 for the protection of neotropical migratory songbird habitat and threatened and endangered species.  Bon Secour represents an important stopover and staging habitat for neotropical migratory songbirds during the fall and spring migration along the Alabama coastline. Migratory birds utilize this area for resting and building fat reserves critical to successful migration. 

The refuge also provides crucial habitat for the endangered Alabama beach mouse that inhabits the beach dune and scrub/shrub habitats found along the Fort Morgan Peninsula. Beach mice have experienced a substantial reduction in available habitat, primarily due to coastal development. Bon Secour National Wildlife Refuge protects the last remaining undisturbed beach mouse habitat found in Alabama, consisting of several key plant communities that form a mosaic of micro-habitats.   

Loggerhead, green, and Kemp's Ridley sea turtles nest on Bon Secour National Wildlife Refuge beaches. Conservation strategies to protect these turtles under the Endangered Species Act include on-site nest monitoring and protection, as well as fostering a public ethic through educational programs.

Bon Secour National Wildlife Refuge is aimed at protecting and preserving these unique habitats and associated wildlife for generations to come. The refuge also serves as a living laboratory for students and scientists, and provides wildlife oriented public recreation.