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 Common mammals include elks, brown bears, wolves, red foxes, European hares, blue hares, red squirrels, lynxes, pine martens, European badgers, as well as American muskrats and minks which were introduced to the area in the early 20th century. About 200 bird species from 15 families have been observed in the lake basin. Lake Onega features a large variety of fish and water invertebrates, including relicts of the glacial period such as lamprey. There are about 47 fish species from 13 families; they include sturgeon, landlocked salmon, brown trout, European smelt, grayling, roaches, Crucian carp, whitefishes, char, pike, European cisco, common