Achieving an acceptable level of anthropogenic impact on ecosystems and biosphere is one of important problems of our time. A system of radiation protection of freshwater ecosystems based on biocenotic effects has not been developed to date. A system of biological monitoring was proposed based on the analysis of the dose-dependent effects identified in the special industrial reservoirs of the Mayak PA at the organismal, population and community levels. This system involves regular assessment and analysis of the state of freshwater biocenoses based on the main dose-forming radionuclide concentrations in the abiotic and biotic components of the ecosystem, estimation of dose rates for the main groups of aquatic organisms, analysis of the state of biocenoses in terms of phytoplankton, zooplankton, zoobenthos, higher aquatic plants, and ichthyofauna. The proposed system complements the industrial environmental monitoring of the Mayak PA and allows solving both scientific and practical problems.