The moderately hilly landscape that contains the Fox River Bottoms IBA historically contained upland tallgrass prairies, oak savannas, and woodland, while today the IBA has cool season pasture, cropland, and substantial tracts of second growth forest on steep slopes (Nigh and Schroeder 2002). Tracts of bottomland forest are also present. Thirty-one percent of the Fox River Bottoms IBA is in publicly owned conservation land, managed by the Missouri Department of Conservation (MDC): Charlie Heath Memorial Conservation Area (CA) (1,647 acres, 667 ha), and Clark CA (393 acres, 159 ha).

Singing male Cerulean Warblers have been observed during their breeding dates on Charlie Heath Memorial CA, within the bottomland along the Fox River, which runs through the IBA. The existing forest provides habitat for many migrant and breeding forest birds, such as Red-shouldered Hawk, Barred Owl, Yellow-throated Warbler, Ovenbird and Kentucky Warbler.

Protection and restoration of bottomland forest may ensure persistence of the Cerulean Warbler and other bottomland forest-dependent species in the Fox River Bottoms IBA. However, restoration of historical prairie, savanna, and woodland habitats within the Wyconda River Dissected Till Plains Ecological Subsection, in which this IBA is located, has been recommended (Nigh and Schroeder 2002).