Lake Onega water per year, of which 46% are industrial and household water, 25% is stormwater runoff and 16% is melioration-related drainage. This drainage contains of phosphorus and of nitrogen; respectively of these elements are removed through the River Svir whereas the rest accumulates in the lake. Ships and motor boats (about 8,000 units) bring oil pollution at the level of about per navigation year, as well as phenols (), lead () and oxides of sulfur, nitrogen, and carbon. The lake basin is a major source of granite, marble and black schist in Russia which have been exploited in the area since
Lake Onega Reservoir has an area of and volume of , i.e. almost the same as those of Onega Lake. Its construction raised the water level of the lake by . The lake contains a well-developed navigation system which is part of the Volga–Baltic Waterway and White Sea – Baltic Canal, connecting the basins of Baltic, Caspian and the northern seas. These canals allow water transport of goods from the lake to the countries from Germany to Iran; most traffic goes to Finland, Sweden, Germany and Denmark. The Onega Canal running along the southern shore of the lake there is not used