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 in its center. Thawing starts in April in the tributaries and reaches the lake in May. Water in the deep parts is clear, with the visibility up to . In the bays, the visibility may decrease to about a meter. The water is fresh, with a salinity of 35 mg/L. This is relatively low for a lake and is about times lower than in the other large lake of the area, Lake Ladoga. The maximum surface water temperature is on the open lake and in the bays. The deep waters are much colder, from in winter to in summer. Weather