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 a total area of about . Whereas the most famous is Kizhi, which contains historical wooden churches of the 18th century, the largest island is Big Klimenetsky with an area of . It contains a few settlements, a school and an hill. Other large islands are Big Lelikovsky and Suysari. The lake banks are low and are flooded with raising water level. They are therefore swampy and are rich in reed, hosting ducks, geese and swans. The coastal region is covered with dense virgin forests. Major tree types are coniferous, but also common are lime (linden), elm and European alder.