ABSTRACT: This paper examines the potential to manage Mississippi River water levels for ecological benefits. The study focuses on the Weaver Bottoms, a 4,000 acre backwater marsh in southeastern Minnesota (Pool 5) highly valued for fish and wildlife habitat. The Weaver Bottoms has suffered increasing loss of aquatic vegetation and associated habitat degradation since the 1960s, largely due to persistent high water, sedimentation, wave re-suspension of sediments, and poor light penetration. In other reaches of the Mississippi River, water level reductions exposing backwater sediments have produced strong vegetative responses due to subaerial exposure of seeds and sediment compaction. Water level management scenarios for Pool 5 were developed using the HEC-2 water surface profile model. Results indicate that in many years it would be possible to reduce water levels sufficiently to expose much of the Weaver Bottoms, generating a substantial vegetative response. Additional benefits could be expected since both sediment compaction and increased vegetation would reduce re-suspension of sediments. Shifting management priorities to improve habitat would temporarily impact many river users, including both commercial and recreational boaters. Water level reductions must be coordinated with their needs.