The results of long-term studies of organic compounds in separated water bodies in two regions: Lake Stepped, Prydz Bay, Commonwealth Sea, (Antarctica) and lakes of the periphery of the Kandalaksha Gulf of the White Sea (the Arctic) are presented. It is established that the eutrophication of these reservoirs largely depends on the connection of these lakes with the sea. Coastal anthropogenic activity affects to a lesser extent. The restoration of the ecosystem of these lakes occurs at the launch of sea waters. The greatest differences between organic compounds in the Arctic and Antarctic waters are established in hydrocarbons. In Antarctica, due to the lack of vegetation, alkanes are dominated by autochthonous compounds, and in the Arctic along with autochthonous, allochthonous.