ABSTRACT: Annual rates of N₂ fixation were measured over 3 yr (1998–2000) at an open water station (BY31) and 2 coastal stations (H4 and X1) in the Baltic Sea. This is the first report on depth-integrated rates of N₂ fixation from more than one complete growth season in the Baltic Sea. Annual estimates of N₂ fixation ranged from 56000 to 125000 t N in the Baltic Proper, and 18000 to 162000 t N at the inshore stations (Himmerfjärden). Rates of N₂ fixation were measured in situ at 4 depths between 0 and 25 m using the ¹⁵N tracer technique for size fractionated organisms larger and smaller than 20 µm. Maximum rates of N₂ fixation were found in surface waters (0 to 4 m depth), and a major part of this activity (80% in coastal and 89% in offshore waters) took place during daylight hours. Integrated rates of N₂ fixation in cells >20 µm followed the average abundance of filamentous cyanobacteria (primarily Aphanizomenon sp.) in the water column. Molar C:N mass ratios in particles >20 µm, i.e. filamentous cyanobacteria, suggest that this size fraction was N-sufficient during summer, whereas the molar C:P mass ratios indicated P-limitation during this period. A reduction in sewage discharge to the Himmerfjärden bay area during the study period appears not to have been compensated for by increased rates of N₂ fixation. The patchy distribution of cyanobacteria and the high seasonal variability in N₂ fixation rates emphasize the need for adequate spatial and temporal sampling strategies in studies of N₂ fixation in coastal and open waters of the Baltic Sea.