Much of the Ottawa National Wildlife Refuge and the surrounding lands were once part of the Great Black Swamp. A vast network of habitats consisting of forests, wetlands, and grasslands, the Great Black Swamp was biologically diverse. Today much of the swamp has been destroyed, and refuge habitat management involves a variety of tools and techniques that mimic the habitat conditions once common within the Great Black Swamp.

The staff at Ottawa Refuge works hard to restore the functions of the Lake Erie marsh ecosystem, which includes marshes, wooded wetlands, estuary, and scrub/shrub. At the same time they are attempting to decrease the exotic plant and animal species present on the refuge that threaten native wildlife.