The species composition and structure of zooplankton and zoobenthos were studied in the Komi Republic’s oldest small storage reservoir, which has operated continuously since 1758. Over the period from 2007 to 2017, 85 species and forms of zooplankton and 21 taxonomic groups of benthic invertebrates were identified. At the initial stage of the research, as the water level in the reservoir was stable and the growth of aquatic macrophytes was minor, the reservoir’s planktic and benthic communities was stable in the species composition and quantities. Lowering of the water level promoted the reservoir’s water trophicity, triggered a rise in the taxonomic abundance and quantities of zooplankton and zoobenthos, a change of the communities’ leading groups, and a reduction in the composition of the dominant complexes. When the water level was boosted up after the restoration of the Kazhimsky hydroelectric installations was over, a vast shore area was flooded, modifying the reservoir’s ecological status. Changes in aquatic invertebrate communities included a decrease in the quantitative indicators of development, a reduction in the number of taxa and species diversity, alteration of the dominant complexes.