The Baltic Sea is a shallow inland sea suffering from heavy anthropogenic pressure. The large cyanobacterial blooms are a visible demonstration of the intense eutrophication of the Sea and have raised public interest in the protection of the Baltic Sea and triggered a heated discussion on the measures that should be taken to counteract eutrophication, such as nitrogen versus phosphorus versus nitrogen and phosphorus removal from the waste waters. A vicious circle seems to operate in the Baltic Sea, with internal feedbacks boosting the eutrophication. A key factor is the effect increasing hypoxia has on the biogeochemical cycles of the nutrients. Phosphorus is released from the sediments during anoxic spells, but the effect on nitrogen is still uncertain. While the nitrogen removing processes, denitrification and anammox, are both anaerobic, they rely on an aerobic nitrification process for substrates. A significant negative relationship exists between the total dissolved inorganic nitrogen and the volume of hypoxic water in the Baltic Sea, indicating enhanced nitrogen removal in hypoxic conditions. To evaluate the role of natural nitrogen removal in current conditions in the Baltic Sea the in situ rates of nitrification and nitrogen removal processes are measured in the water column. Samples will be collected on research cruises. Stable isotope techniques will be used for measuring denitrification and anammox and regulation of these . Additionally isotopic fingerprinting will be used to study the role of nitrification-denitrification . Several approaches will be used to quantify in situ nitrification, including stable isotope ammonium oxidation coupled to denitrifier-based NO3 analysis , specific inhibitor use (N-serve, allylthiourea (ATU), acetylene, methylfluoride) and 14CO2-microautoradiography . To clarify the environmental conditions needed for the efficient co-operation of these processes additional experimental research will be done, and environmental databases will be used to map the actual volume of water in which such conditions exist. The information gained will be used to improve the accuracy of the biogeochemical components of large ecosystem models such as Nest (Baltic Nest Institute, Stockholm Resilience Centre) and RCO-SCOBI (Swedish Meteorological and Hydrological Institute). That, in turn, will reduce the uncertainty in the models used for calculating the costs and effects of possible nutrient reduction measures. Additionally, models with a better description of the factors regulating nitrogen removal can be used to predict how the self-purification (nitrogen removal) capacity adjusts to changes in the ecosystem, such as climate change or increase or decrease in nutrient loading.