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
Onega River Monastery on an island in the Lake Kozheozero. Some of the finest monuments of the northern wooden architecture are located in the basin of the Onega, including ensembles of Lyadiny, Saunino Pogost, Krasnaya Lyaga, and Bolzhaya Shalga. These monuments also suffer from the lack of protection and their number steadily diminishes. In fact, the majority of them have been lost. The river splits into the Big Onega and Little Onega Rivers from its estuary, but then these branches join again, forming a big flat island. It freezes up in late October - early December and stays under the ice until