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 months. The highest water level is in June–August and the lowest is in March–April. Rivers bring of water per year to the lake, that is up to 74% of the water balance; the rest is provided by precipitation. Most of the lake water (84% or per year) outflows via a single River Svir, and the remaining 16% evaporates from the lake surface. There are frequent storms more characteristic of a sea than a lake; waves of are not uncommon and may even reach . The lake freezes near the coast and bays in late November and December and around mid-January