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 dace, silver bream, carp bream, sabre carp, spined loach, wels catfish, European eel, rudd, ide, gudgeon, pike-perch, European perch, ruffe and burbot. Whereas the area of the lake used to be clean, the pollution level is gradually increasing, especially in the northwestern and northern parts which contain the industrial facilities of Petrozavodsk, Kondopoga and Medvezhyegorsk. About 80% of the population and more than 90% of industry of the basin are concentrated in these areas. The pollution from these three cities amount to about of sewage and drainage water and of emissions per year. Human activity results in about of drain