As climate change is expected to be extremely intense in the Arctic Ocean there is an utmost need to study food-web interactions to contribute to a better understanding of the direction and strength of biogeochemical and microbiological feedback processes. Climate change induced alterations will directly affect food-web structures and ecosystem functioning. Recent studies indicate that environmental changes like increasing temperatures as well as freshening of surface waters promote a shift in the phytoplankton community towards a dominance of smaller cells, especially of eukaryotic picoplankton. The response of oceanic ecosystems and marine carbon cycling to these changes is particularly determined by microbial loop activity. Heterotrophic bacteria, as part of the microbial loop and a crucial component of marine food webs, have a key role in controlling carbon fluxes in the oceans. Microbial activities, dynamics and diversity were studied in the area of the deep-sea long-term observatory HAUSGARTEN of the Alfred-Wegener-Institute (Fram Strait) in July 2009. The investigation area is located within a transition zone between the northern North Atlantic and the central Arctic Ocean, which separates the warm and cold water masses originating from the West Spitzbergen and the East Greenland currents. While bacterial abundance and chlorophyll a were tightly coupled, differences of the planktonic and bacterial community structures are most likely due to the heterogeneous hydrography. Warmer water masses comprise a higher genetic diversity of picoplankton, as it is also expected for bacteria. A shift towards a dominance of smaller plankton species can potentially affect the quality of organic matter and subsequently microbial cycling. Here we present data on bacterial abundance, biomass and protein production, hydrolytical enzyme activities and community structure within different size classes with respect to changing biotic and abiotic conditions in the Fram Strait.