High-head dams throughout the Willamette River Basin, Oregon create deep reservoirs that undergo inter-seasonal and intra-seasonal water-level fluctuations (WLFs). The magnitude of WLFs is dependent on competing objectives of flood control, recreation, and water releases to maintain downstream habitat and facilitate migration of Endangered Species Act-listed salmonids. These reservoirs are drawn down to minimum conservation pool in winter, refilled to full pool by late spring and undergo variable WLFs, typically between 4 and 15 m, throughout summer. Here, we investigate the impact of seasonal WLFs on the density, biomass, and species composition of littoral benthic macroinvertebrates at Fall Creek, Hills Creek, and Lookout Point reservoirs. We sampled the submerged littoral zone during spring and summer using an adapted quadrat sampling method and assessed differences in species assemblages using a nonparametric multivariate statistical technique. Descriptors of variation in substrate, WLF, temperature, and depth were incorporated to identify environmental variables associated with variation in assemblage composition. We hypothesized that density and biomass would decrease and assemblage composition would shift between seasons in response to WLFs. We found statistically significant differences in assemblage composition between seasons and among reservoirs, but density and biomass did not respond similarly. Observed variation in assemblages was associated with surface water temperature, water depth, substrate, and WLF. None of these variables alone explained observed variation. We provide evidence that seasonal WLFs influence macroinvertebrate assemblage composition and alter habitat characteristics. Our procedure effectively quantifies changes in species assemblages in impounded systems with low densities and dynamic littoral zones and can inform water management decisions with relatively modest costs.