The Mississippi Alluvial Valley (MAV) had extensive bottomland hardwood forests but less than 25% of this area remains forested today. Impounded greentree reservoirs (GTRs), have been managed for wintering waterfowl since the 1930s, and provide a source of aquatic invertebrates and acorns for foraging ducks and other wildlife. However, few studies of invertebrate community-composition, diversity, and biomass have been conducted at regional scales. We collected samples of aquatic invertebrates from three hardwood bottomlands in the MAV and one in the Mississippi Interior Flatwoods region during winters 2008-09 and 2009-10. We compared community composition metrics of aquatic invertebrates between naturally flooded forests (NFF) and GTRs. Five families occurred more frequently in GTRs than NFFs (P < 0.01); these were Asellidae, Chironomidae, Cragonyctidae, Daphniidae, and Sphaeriidae. However, the NFFs had greater invertebrate familial diversity than their paired GTRs for most winter months. Across winters, we found most invertebrate families (65% [early winter] and 82% [late winter]) associated with sites in NFFs and GTRs with depths from 10-40 cm. Because GTRs are typically flooded to depths greater than this range, and flooding of most GTRs results in relatively stable hydroperiods, we re-emphasize need for managing hydrology of GTRs similarly to local NFFs, which may promote increased invertebrate diversity and biomass.