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 the last Ice Age, about 12,000 years ago: In the Paleozoic Era (400–300 million years ago) the entire territory of the modern basin of the lake was covered with a shelf sea lying near the ancient, near-equatoric Baltic continent. Sediments at that time – sandstone, sand, clay and limestone – form a layer covering the Baltic Shield which consists of granite, gneiss and greenstone. The retreat of the Ice Age glaciers formed the Littorina Sea. Its level was first higher than at present, but it gradually lowered, thereby decreasing the sea area and forming several lakes in the Baltic region.