Many of the organisms in the Bothnian Sea live close to their limit of tolerance with respect to salinity and temperature. The shallow sill area of the Quark acts as a barrier for marine animal and plant species and represents a northern boundary of distribution for many organisms. Bladder wrack (Fucus vesiculosus L.), bay barnacle (Balanus improvisus), common mussel (Mytilus edulis), cockle (Cerastoderma glaucum) and several species of crustaceans do not occur in the Bothnian Bay. A waterfowl species, the common eider (Somateria mollissima), is only scarce.

The growth season in the Bothnian Bay is hardly half as long as in the southern parts of the Baltic Sea owing to the ice cover, darkness and coldness of the long winter. Regardless of having enough light and nutrients needed for photosynthesis during the short summer, the total phytoplankton production is only one fourth of that in the Bothnian Sea. Mainly freshwater diatoms bloom in the Bothnian Bay. This bloom occurs as late as in June because of the long period during which the area is covered with ice. The ice, however, not only restrains life, but also promotes it as some phytoplankton species are adapted to living beneath the ice on its surface or in channels inside the ice. This phytoplankton is exploited by bacteria, zooplankton and other microscopic organisms. There are about five zooplankton species in the Bothnian Bay. Of them, copepods and cladocerans are an important source of nutriment for Baltic herring and sprat.

The low phytoplankton production indicates that photosynthesis is not sufficient enough to produce all the energy needed in the Bothnian Bay. The organic material and the nutrients that the rivers transport into the Bothnian Bay serves as an extra source of energy and nutrients for the heterotrophs of the area.