Wildlife habitat on the Complex is extremely important to conservation of waterfowl, bald eagles, and grassland birds. The Complex occupies the southern portion of the Prairie Pothole Region - also known as the "Duck Factory." Many ducks rely on this habitat to successfully raise their young. The area also hosts migrant waterfowl populations in the tens and hundreds of thousands during peak fall and spring migration periods. The Karl E. Mundt NWR provides important habitat for 100-300 bald eagles. The Refuge protects one of the most critical bald eagle winter roosts in the country. Waterfowl and other ground-nesting birds also benefit from wetlands and grasslands protected on the Lake Andes WMD.

Grasslands surrounding Owens Bay are managed to provide cover for nesting waterfowl. Periodic grazing, prescribed burning, haying, reseeding, and herbicide spraying are necessary to keep grasses vigorous and free of noxious weeds. High densities of waterfowl nest in these grasslands.

Waterfowl production areas on Lake Andes WMD are managed similarly to Lake Andes NWR. Wetlands are generally smaller and subject to even more rapid wet and dry cycles than on Lake Andes. Cooperating farmers conduct grazing and haying.

Bald eagle conservation is the focus of the Karl E. Mundt NWR. The Refuge is closed to public use to protect eagles from disturbance when they are most sensitive - roosting during the cold heart of winter and nesting during spring, summer, and fall. Dams on the Missouri River have changed river ecology to the degree that cottonwoods no longer replace themselves along the river banks. Since these trees are important to bald eagles for roosting and nesting, they are replanted on the Refuge periodically.