The Kuetsjärvi lake ecosystem has been subject to intensive pollution generated by the Pechenganickel Company activities for more than 50 years. This article considers the effects of emissions from the copper-nickel smelter, that uses out-of-date technology, on a subarctic lake ecosystem. Six years of investigations revealed changes occurring at all ecosystem levels. It was found that the content of heavy metals (Cu, Ni, etc.) in lake sediments was dozens of times higher than the background values. Phyto- and zooplankton communities were in an unstable condition, while fish had pathologies of functionally important organs (gill, liver and kidney). The concentration of nickel in zoobenthos and fish was correlated its accumulation in sediments.