The effects of nutrient load reductions on the biomass of N-fixing cyanobacteria were evaluated in the scale of the Gulf of Finland. The two analysed reduction scenarios were Finnish national agenda and the improvement of phosphorus removal in the present purification plants of St. Petersburg. The effects of load reduction scenarios were tested by using a 3D-ecosystem model with a horizontal resolution of 5 km. According to the results the Finnish national agenda cannot decrease the biomass of N-fixing cyanobacteria, but it seems to be able to reduce the total phytoplankton biomass in the coastal waters. The phosphorus reduction in St. Petersburg decreases the N-fixing cyanobacteria significantly in the central parts of the Gulf of Finland. Improvement of the phosphorus purification efficiency in the present sewage treatment plants offers us an opportunity to try to control the intensity of the toxic blooms of nitrogen-fixing cyanobacteria in the scale of the Gulf of Finland.