Historically the area encompassing the Lincoln Alluvial Complex was mostly wet prairie and marshland, with some bottomland forest along rivers and islands (Nigh and Schroeder 2002). Though much of the region was plowed to cropland, marshland and bottomland forest still exist, protected on many conservation landholdings.
Fifty-six percent of the IBA is publicly-owned conservation land. Included in the IBA are Clarence Cannon National Wildlife Refuge (3,750 acres, 1,518 ha), managed by the US Fish and Wildlife Service, and the following Missouri Department of Conservation areas: B. K. Leach Memorial Conservation Area (4,335 acres, 1755 ha), Prairie Slough Conservation Area (610 acres, 247 ha), and Upper Mississippi Conservation Area (2,327 acres, 942 ha).
The wetlands in the Lincoln Alluvial Complex provide habitat for many migrant and breeding waterbirds. Nesting records on Clarence Cannon National Wildlife Refuge (NWR) include American and Least Bitterns, Bald Eagles, Common Moorhen, Marsh Wren, and Virginia Rail. Sora have also been observed during breeding season at the NWR. King Rail have been confirmed nesting at the north unit of B. K. Leach Memorial Conservation Area (CA) and adults have been observed during the breeding season at Prairie Slough CA. Least Bitterns also nest at B. K. Leach Memorial CA (north unit). Large concentrations of migratory waterfowl and shorebirds also utilize the wetland pools and mudflats within this IBA each year. This IBA is also located along a major flyway for neotropical migratory songbirds, which utilize the bottomland forest habitats in the IBA for stopover sites.
On Clarence Cannon NWR, a spillway was constructed along a levee bordering the Mississippi River, which allows periodic flooding of the refuge. Water levels are manipulated among pools on the NWR, and prescribed burns and disking are used to maintain marshland in an early successional state. Despite tree die-offs from the Great Flood of 1993, 450 acres of bottomland forest remain on Clarence Cannon NWR. Recently established emergent marsh units at B. K. Leach Memorial CA have also shown great promise.