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
Arkhangelsk Oblast the south-west of the Oblast drains into the Kema River which belongs to the basin of the Caspian Sea. The area in the Onega River basin containing the biggest lakes in the oblast, such as Lake Lacha, Lake Kenozero, Lake Undozero, and Lake Kozhozero. The tundra of the Nenets Autonomous Okrug also contains a number of bigger lakes. The river basin of the Pinega is characteristic of the karst, with a number of caves in the region. The White Sea coast within the Oblast is split into the Onega Bay (where the Onega is the major tributary), the Dvina Bay