The lake drains into the Baltic Sea through the Hohenfelder Mühlenau, only 10 km long, to the north and by the Salzau to the northwest.

The formation of the Selenter See goes back to the ice sheets of the Weichselian glaciation, which hollowed out a basin and simultaneously formed ridges of terminal moraine up to 132 m high in the east and 90 m high in the south.

The lake is well-known inter alia for plentiful supply of fish such as eel, perch, pike, and large and small whitefish and large quantities of roach.

There is a 3,060 hectares (7,600 acres) bird reserve called the Selenter See-Gebiet which covers the lake and its bordering reed beds and carr areas as well as the Gottesgabe Wood.

It is an important breeding, moulting and resting area for numerous birds including the kingfisher, bittern, whooper swan, goosander, great crested grebe, crane and sea eagle.