Within the aquatic environment we find a major richness of microbial species, driving essential nutrient cycles. The composition of these communities can be very sensitive towards environmental shifts like changes in temperature, nutrients or salinity. The waters of the Danish Straits form a salinity gradient were brackish water from the Baltic Sea mixes with the saline water from the North Sea. Additionally the Baltic is a highly eutrophic environment. The aim of this study is to find out if different bacterial communities are present in the North- and Baltic Sea and which environmental variables are responsible for this. Sampling and filtering of surface water and measurements of environmental variables took place on stations in the North Sea, Skagerrak, Kattegat and western Baltic Sea. DNA was extracted from two size fractions (separating particle-attached and free living bacteria). DNA was extracted and the bacterial 16S rRNA intergenic spacer regions were amplified by PCR. Bacterial community fingerprints were obtained through Automated Ribosomal Intergenic Spacer Analysis (ARISA). Statistical analysis showed the presence of different communities within the North- and Baltic Sea. This distribution is mainly caused by salinity and to a smaller degree by the concentration of dissolved organic carbon, while temperature and primary producing biomass had no significant influence. Not all the significant factors have been identified. A comparison between the two size fractions revealed a significant difference between the bacteria communities living attached to particles and those living in the water column as well.