The Long-Term Ecological Research (LTER) site HAUSGARTEN located in the eastern Fram Strait (79°N, 4°E) was established in 1999. Since then, year-round measurements of physical properties of the surface ocean and water column were carried out as well as biogeochemical and biological measurements of carbon fluxes to the seafloor. During a warm period in the years 2005-2007, a shift in the phytoplankton community and a decrease in phytodetritus export took place. In this study we further investigated how the dynamics of the sea ice cover and biological pump affected benthic bacterial community composition and activity. Bacterial community diversity was determined by Illumina tag sequencing. The changes in food supply caused by warming were reflected in shifts of bacterial types at the seafloor, resulting in interannual dynamics of the bacterial community structure. Our results indicate an immediate response of the benthic community to changes in surface ocean conditions, indicating that surface ocean dynamics induced by climate change are directly reflected at the seabed.