The Finger Lakes habitat-rehabilitation project is intended to improve physical and chemical conditions for fish in six connected back water lakes in Navigation Pool 5 of the upper Missouri River. The primary management objective is to improve water temperature, dissolved oxygen concentration and current velocity during winter for bluegills, Lepomis macrochirus, and black crappies, Pomoxis nigromaculatus, two of the primary sport fishes in the lakes. The lakes will be hydrologically altered by Installing culverts to Introduce controlled flows of oxygenated water into four lakes, and an existing unregulated culvert on a fifth lake will be equipped with a control gate to regulate inflow. These habitat modifications constitute a manipulative field experiment that will compare pre-project (1991 to summer 1993) and post-project (fall 1993 to 1996) conditions in the lakes, including hydrology, chemistry, rooted vegetation, and fish and macroinvertebrate communities. Initial data indicate that the Finger Lakes differ in water chemistry, hydrology, and macrophyte abundance. Macroinvertebrate communities also differed among lakes: species diversity was highest in lakes with dense aquatic macrophytes. The system seems to support a single fish community, although some species concentrated in individual lakes at different times. The introduction of similar flows into five of the lakes will probably reduce the existing physical and chemical differences among lakes. However, our ability to predict the effects of hydrologic modification on fish populations is limited by uncertainties concerning both the interactions of temperature, oxygen and current in winter and the biological responses of primary and secondary producers. Results from this study should provide guidance for similar habitat-rehabilitation projects in large rivers.