Currently the Arctic is severely affected by global warming. Summer minimum sea ice extent is shrinking and estimates of sea ice thickness also indicate a rapid decrease. Whether such changing sea ice conditions affect biodiversity and functioning of bacterial communities from sea ice, melt pools, and surface water was studied during a summer expedition in 2011 in comparison to earlier studies in 1997 and 1999. The route of the 2011 cruise lead to the Central Arctic Ocean thus samples of Atlantic as well as Pacific influenced water could be taken. In the Atlantic influenced area higher secondary production rates, determined by means of thymidine incorporation, were obtained in comparison to the Pacific influenced area. Bacterial activities of the sea ice samples in the Atlantic section exceeded in most cases those of melt pools while in the Pacific section melt pools and upper ice samples were more active than the deeper ice layers. However, especially in the Atlantic influenced area, a high percentage of the melt pools were covered by big yellow/orange aggregates. Such amounts of visible organic matter were not observed during the cruises in 1997 and 1999. The differences in bacterial activites were found to be reflected in the phylogenetic bacterial community compositions that were analysed based on 16S rRNA-gene clone libraries and amplicon sequencing as well as CARD-FISH. In the Atlantic influenced area gammaproteobacteria were found dominating while in the Pacific influenced area betaproteobacteria or alphaproteobacteria were abundant. Further, differences between the bacterial communities in 2011 and 1997 were tried to detect by means of temperature adaptation studies.