The Bothnian Bay stretches out from Kvarken in the south to its northernmost point in the Torne River estuary in the Tornio–Haparanda area. There are very few islands on the coastline of the Bothnian Bay, and sandy seabeds are common. The shorelines of the islands are rocky, but there are hardly any rocky beaches in the area. Post-glacial rebound continues to have a strong impact on the coastline of the Bothnian Bay. Many major rivers flow into the Bothnian Bay, including the largest salmon river of the Baltic Sea, i.e. the Torne. Each year, a significant number of the salmon in the Baltic Sea run via the Bothnian Bay to spawn. Other great rivers that flow into the Bothnian Bay include Kemijoki, Oulujoki, Luulajanjoki and the Kalix.
The salinity of the surface waters of the Baltic Sea diminishes towards the north, and in the Bay of Bothnia, just like in the eastern end of the Gulf of Finland, the water of the Baltic Sea is actually almost fresh. The number of species that thrive in the Baltic Sea also diminishes when we move from southern Baltic Sea towards the north. The low salinity of the northern Baltic Sea, cold winters, and the sea freezing over all pose challenges for animal and plant adaptation. The Bothnian Bay is relatively low in nutrients, and since the load caused by humans is also lower than in other areas of the Baltic Sea, the Bothnian Bay and Kvarken are home to the only parts of the Baltic Sea that can currently claim to have a good status (Helcom).