1. The internal cycles of carbon, nitrogen and phosphorus in the Baltic Sea are, like in other seas, mainly controlled by biological production and degradation of organic matter (OM).

2. Biological activity also modulates the acid/base balance (pH), which is mainly a function of alkalinity and the total CO2 concentration.

3. Particulate organic matter (POM) produced in the photic zone sinks into deeper water layers and is deposited on the sediment surface, where it is mineralised. Mineralisation is a form of microbial oxidation and thus leads to oxygen depletion. Due to its semi-enclosed position and its bottom topography, large-scale oxygen depletion of deep bottoms is common in the Baltic Sea.

4. Under anoxic conditions, the burial of phosphorus bound to ferric oxide is inhibited and the availability of phosphate for incorporation in new OM production increases.

5. In stagnant waters, the oxic/anoxic interface may migrate from the sediment into the water column, forming a pelagic redoxcline. Such a redoxcline occurs in large areas of the Baltic Sea.

6. At oxygen concentrations close to zero, nitrate acts as an oxidant and is reduced to elemental nitrogen (denitrification). After the exhaustion of both oxygen and nitrate, OM is oxidised by sulphate, which is reduced to toxic hydrogen sulphide.

7. The final step in the mineralisation process is the microbial formation of methane in deeper sediment layers, which reflects the internal oxidation/reduction of OM.

8. A significant fraction of the organic carbon, nitrogen and phosphorus escapes mineralisation and is permanently buried in the sediment. On a long-term basis, this loss, together with export to the North Sea and internal sinks, is mainly balanced by riverine inputs and atmospheric deposition to the Baltic Sea.