<p>Over the next decade, the Baltic Sea is predicted to undergo severe changes including a decrease in salinity due to altering precipitation. This will likely impact the distribution and community composition of Baltic Sea N<sub>2</sub> fixing microbes, of which especially heterocystous cyanobacteria are adapted to low salinities and may expand to waters with currently higher salinity, including the Danish Strait and Kattegat, while other high-salinity adapted N<sub>2</sub> fixers might decrease in abundance. In order to explore the impact of salinity on the distribution and activity of different diazotrophic clades, we followed the natural salinity gradient from the Eastern Gotland and Bornholm Basins through the Arkona Basin to the Kiel Bight and combined N<sub>2</sub> fixation rate measurements with a molecular analysis of the diazotrophic community using the key functional marker gene for N<sub>2</sub> fixation <em>nifH</em>, as well as the key functional marker genes <em>anf</em> and <em>vnf</em>, encoding for the two alternative nitrogenases.</p> <p>We detected N<sub>2</sub> fixation rates between 0.7 and 6 nmol N L<sup>-1</sup> d<sup>-1</sup>, and the diazotrophic community was dominated by the cyanobacterium <em>Nodularia</em> and the small unicellular, cosmopolitan cyanobacterium UCYN-A. <em>Nodularia</em> was present in abundances between 8.07 x 10<sup>5</sup> and 1.6 x 10<sup>7</sup> copies L<sup>-1</sup> in waters with salinities of 10 and below, while UCYN-A reached abundances of up to 4.5 x 10<sup>7</sup> copies L<sup>-1</sup> in waters with salinity above 10. Besides those two cyanobacterial diazotrophs, we found several clades of proteobacterial N<sub>2</sub> fixers and alternative nitrogenase genes associated with <em>Rhodopseudomonas palustris</em>, a purple non-sulfur bacterium. Based on statistical testing, salinity was identified as the primary parameter describing the diazotrophic distribution, while pH and temperature did not have a similarly significant influence on the diazotrophic distribution. While this statistical analysis will need to be explored in direct experiments, it gives an indication for a future development of diazotrophy in a freshening Baltic Sea with UCYN-A retracting to more saline North Sea waters and heterocystous cyanobacteria expanding as salinity decreases.</p>