Lake Onego is the second largest lake in Europe next to Lake Ladoga. The lake basin is situated on two contrasting parts of the earth crust with different geological histories, Baltic shield and Russian plate. The boundary runs approximately along the line connecting the mouths of the Vodla River and the Shuja River. To the north of the boundary, the shoreline is extremely jagged, and the greater part of islands and numerous fjord-type bays are found. The northern basin is surrounded by hills and cliffs consisting of crystalline rocks. There, land relief forms are oriented from northwest to southeast, following the direction of ice flow during glacial periods. Deep hollows (90 - 100 m deep) are interspersed with ridges only 1-2 m below the water surface. The southern basin is relatively shallow with a mean depth of 30 m and more or less flat bottom. Shorelines are less jagged, and are frequently covered by marsh.

Tectonic processes in the pre-glacial period, combined with glacial erosion and transport, formed the specific hydrographical network. The history of Lake Onego experienced several glacial periods, when its flora and fauna were exterminated. The last glaciation ended 11,000-12,000 years ago. The lakeshore became inhabited some 9,000 years ago. Some 800 rock drawings or so-called petrogliffs, which were made from the end of the third to the beginning of the second millennium B. C., are invaluable heritage in the history of human culture. On the lake shore, there are also a number of wood architectures of 17-18th centuries including world-famous Kizhi-ensemble.

Lake Onego is now the source of freshwater of high quality (total mineral concentration 34-36 mg l^-1). It also forms part of the major waterborne transport system in the USSR, and serves as a reservoir for hydroelectric power generation and an important fishing ground.