Lake Onega is relatively cold, with temperatures below for half of the year and average summer temperatures of about . The catchment area of drains into the lake via 58 rivers and more than 110 tributaries, including the Shuya, Suna, Vodla, Vytegra and Andoma. The only outgoing River Svir, which marks the southern boundary of Karelia, runs from the southwestern shore of Lake Onega to Lake Ladoga and continues as the Neva River to the Gulf of Finland. The White Sea–Baltic Canal runs through the lake from the White Sea to the Baltic Sea. The Volga–Baltic Waterway connects Onega Lake with the
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