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
White Sea–Baltic Canal waterway length is , of which are man-made. The current flows north from Lake Onega to the White Sea, and all navigation marks are set according to it. Once in Lake Onega, ships can exit the southwest shore through the Svir River (and its two locks) to reach Lake Ladoga and then proceed down the Neva River to Saint Petersburg and the Baltic Sea. Alternatively, from Lake Onega river ships can sail eastward into the Volga–Baltic Waterway. The canal begins near Povenets settlement in Povenets bay of Lake Onega. After Povenets there are seven locks close together, forming the "Stairs