The effects of water-level regulation on aquatic macrophyte communities, individual plant species, and potential faunal habitat were investigated in a study of two regulated lakes and an unregulated lake in northern Minnesota. Water levels in Rainy Lake and Namakan Reservoir in Voyageurs National Park are regulated by dams. Natural annual fluctuations of 1.8 m are replaced with fluctuations of 1.1 m in Rainy Lake and 2.7 m in the five lakes that comprise Namakan Reservoir. In addition, springtime peaking of water levels in Namakan Reservoir is delayed by one month. After reaching the peak, water levels in the regulated lakes are held at that level through the summer and allowed to gradually decline through autumn and winter. This study was conducted by estimating the cover of each plant species in randomly placed quadrats along transects that followed depth contours in the lakes. These contours were selected to represent different plant habitats, as defined by the timing and duration of flooding and dewatering in unregulated Lac La Croix. Detrended correspondence analysis showed that the macrophyte communities at all depths of the regulated lakes differed from those in the unregulated lake. The differences were more profound in deeper parts of the littoral zone. Lac La Croix contained taxonomically and structurally diverse plant communities at all depths, maximizing faunal habitat. The greatest effect of the regulation on Rainy Lake was along transects at the depth that is never dewatered. There were only four taxa present; they were all erect aquatics that extended through the entire water column and offered little structurally diverse faunal habitat. The greatest effect of regulation on Namakan Lake was along transects at the depth where drawdown occurs in early winter and disturbance results from ice formation in the sediments. Rosette and mat-forming species were dominant, providing minimal faunal habitat. The hydrologic regime at Lac La Croix results in intermediate disturbance that maintains high diversity. There is too little disturbance from water-level fluctuations in Rainy Lake and too much disturbance in Namakan Reservoir, resulting in reduced diversity in both cases. The macrophyte communities of the regulated lake systems would benefit from a return to more natural hydrologic regimes. Namakan Reservoir should be regulated to reach its peak water level at the beginning of June, summer drawdowns should occur at both Rainy Lake and Namakan Reservoir, and the amplitude of annual drawdowns should vary between years but approximate 1.8 m. These hydrologic conditions should, over time, result in more diverse macrophyte communities and more diverse faunal habitat throughout the littoral zone of the regulated lakes.