Habitats include forests, open fields, freshwater impoundments, and estuarine tidal wetlands. More than 250 bird species, including the American bald eagle and peregrine falcon, as well as the endangered Delmarva fox squirrel, can be found at Blackwater for at least a portion of the year.

Since 2003, the Aquarium Conservation Team (ACT!) has worked in the refuge to restore wetland habitat and plant trees with community volunteers, students, and local environmental groups, including the Friends of Blackwater. ACT! continues to visit these sites to monitor their progress.

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