We have shown the changes in the ecosystem of Lake Onego 1 with climate warming over the past 30 years. Due to climate warming in winter, the river runoff increases, as well as the flow of allochtonic substances into the lake. With the increased runoff of the Shuya River, the main tributary of the Petrozavodskaya Guba (Bay), there is an additional influx of iron and phosphorus to the lake combined with the humus substances. Deep-water benthic communities in the lake become depressed. Therefore, in the past three decades the role of climate warming in the aquatic ecosystem has increased in comparison with anthropogenic impacts, which differs significantly from the changes in previous decades.