The entire Baltic Sea, as well as many of its different sub-regions, are subject to eutrophication due to high nutrient inputs. To plan expensive water management measures one needs a tool to quantify effects of different water management policy decisions. The tools implemented here are simulation models based on similar descriptions of biochemical interactions in the water and sediments but coupled to different hydrodynamical models. For the Baltic Proper a 1D physical model with high vertical resolution but horizontally integrated was used. Simulations for 20 years made with 50% load reduction each 5 year show that for this domain and at these scales the recovery would take decades. The most effective is reduction of phosphorus, while reduction of only nitrogen leads to a dramatic increase in cyanobacteria blooms. For the Gulf of Finland a high-resolution 3D hydrodynamic model was coupled to a more crude 3D-box biogeochemical model describing concrete conditions during August and November 1991. In the Eastern Gulf of Finland the effects of a 50% load reduction from the St. Petersburg region are pronounced even after two weeks. Here, nitrogen reduction would be more beneficial than that of phosphorus, both locally and at a larger scale. The conclusion from these simulations is that the difference in effects of nitrogen versus phosphorus reduction is dependent on scales and locations of management.