This paper presents integrated research on ecosystems of small lakes experiencing the direct impact of a copper-nickel ore processing plant, the &ldquo / Kolskaya GMK&rdquo / (MS KGMK), near the town of Monchegorsk Kola Peninsula, Russia. An integrated research method with the analysis of both abiotic and biotic components of aquatic ecosystems was used. It was found that the water ecosystems developed under the conditions of extreme pollution depleted the species composition of the hydrobionts and the number indices. Much of the pollution resulted in a transformation in the phytoplankton community structure: the share of mixotrophic algae and Cyanobacteria increased. Anthropogenic eutrophication resulted in a decrease in toxic impact. Despite high anthropogenic load, Salmonid and Coregonid species were found in a number of water bodies. The size and weight indices and the heavy metal accumulation intensity had a distinct gradient nature. The macrozoobenthos in the water bodies studied was characterized by depleted taxonomic composition and extremely low numbers. The basis of the zoobenthos was formed by chironomids Psectrocladius, Procladius, Cricotopus, and Orthocladius, spread widely in water bodies polluted with heavy metals.