The Illinois and central Mississippi river valleys provide important habitats for migrating waterfowl. Unfortunately, both river systems have experienced large-scale hydrologic alterations, resulting in considerable loss of waterfowl habitat. To provide information to guide wetland conservation and rehabilitation efforts, we used data from aerial inventories of waterfowl conducted by the Illinois Natural History Survey to model Mallard (Anas platyrhynchos) use in relation to wetland characteristics. Mallard use was positively associated with the proportion of wetland area classified as “emergent” (e.g., containing robust or moist-soil wetland vegetation) during spring and fall in both river valleys. Use by Mallards was also related to proportion of inventoried locations where hunting and other disturbances were prohibited during fall and spring, perhaps indicating better management of fall refuges to provide foraging habitat during spring. We suggest wetland habitat acquisition and rehabilitation efforts intended to benefit waterfowl emphasize emergent-wetland components. Further, we recommend investigations of wetland use by waterfowl in each river system to elucidate the role of areas where hunting and disturbance is prohibited.