We investigated the role of water level fluctuation on benthic macroinvertebrate communities of stony littoral habitats located in the Boreal Shield Ecozone. Using the reference condition approach (RCA), regression analysis, nonmetric multidimensional scaling (NMDS), and analysis of variance (ANOVA), we analyzed the benthic macroinvertebrate community structure of 20 natural lakes and 28 hydroelectric reservoirs to determine if they are structured by change in water level (amplitude). Along a gradient of amplitude intensity, we found that taxa richness decreases with increasing amplitude (r2 = 0.47–0.60). Littoral benthic macroinvertebrate community structure is significantly different in reservoirs that experience amplitudes > 2.0 m. Out of 28 reservoirs, 13 fell outside the 95.5% confidence ellipse determined by 20 reference lakes. Functional mobility group and functional feeding group composition are also altered with increasing amplitude (nonparametric ANOVA, P < 0.05). Further, a change in benthic macroinvertebrate functional composition occurs after a change in taxa richness. Interestingly, reservoirs that experienced amplitudes < 2.0 m had benthic macroinvertebrate communities whose structural and functional composition is similar to lakes experiencing natural water level fluctuations.