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 area containing the Kondopozhskaya (, depth up to ), Ilem-Gorskaya (), Lizhemskoy () and Unitskoy () bays. To the southwest of Greater Onega lies Petrozavodskoye Onego () containing the large Petrozavodsk and small Yalguba and Pinguba bays. To the east of Zaonezhye there is a bay, northern part of which is called Povenetsky Bay and the southern part is Zaonezhsky Bay. There, deep sections alternate with banks and islands which split the bay into several parts. The southernmost part of them, Lesser Onega, is deep. All the shores there are rocky. The average depth of the lake is , and