The refuge serves as a resting and feeding area for migratory birds and as a sanctuary for native flora and fauna.

Established in 1980, Bon Secour (the name, in French, means "safe harbor") is smaller than most other national wildlife refuges, and is divided into Sand Bayou, Perdue, Little Point Clear, Fort Morgan, and Little Dauphin Island.

[2] Bon Secour suffered extensive damage on 16 September 2004 due to a near direct hit from Hurricane Ivan and the accompanying 20-foot (6 m) storm surge.

Debris cluttered the Jeff Friend unit, while the Pine Beach trail suffered the loss of both the Gator Lake boardwalk and observation pavilion.

After cleaning up a second wave of less-extensive damage from Hurricane Katrina, limited access to the refuge beach in the Purdue unit reopened in October 2005.