Fish in the Blackwater River and the Little Blackwater River play an important role in providing food for numerous species including herons, bald eagles and ospreys. Fish species at the Refuge include tidal largemouth bass (black bass), striped bass (rock fish), white and yellow perch, black crappie, and bullhead and channel catfish. Other species available in the waters of the Refuge are carp, blue gill and pickerel.

Rare fish species associated with Blackwater Refuge include the American eel, glassy darter, comely shiner, mud sunfish, blackbanded sunfish, and Atlantic sturgeon.