Nitrogen fixation is a major nitrogen source for the open ocean. Also the land-locked, partly anoxic Baltic Sea receives almost as much nitrogen from nitrogen fixation as it receives from eutrophied rivers. Growth conditions for cyanobacteria are usually very favorable with low N/P ratios after winter mixing and a strong stratification and high surface temperatures in summer. However, the summer 2012 was quite different with strong winds and cold surface waters. Blooms of cyanobacteria therefore only developed in sheltered regions but not in the central Baltic Proper. Moreover, a greater variety in nitrogen fixing species than usual was observed. Under these conditions nitrogen fixation rates were studied over a three weeks period throughout the upper water column. Moreover, a methods comparison was performed to test the dissolved dinitrogen gas additions against the bubble addition. Different incubation lengths and starting times of the incubation in relation to the daily cycle of nitrogen fixation were considered to receive a best estimate of fixed nitrogen under these specific conditions.