The anthropogenic emissions of CO2 and other climate-active gases lead to a steep increase of global temperatures. Global climate change is particularly amplified in the Arctic (e.g., Serreze et al., 2009; Serreze and Barry, 2011). Increasing temperatures and the rapid sea ice decline have shown profound effects on life in the Arctic ecosystem (Wassmann et al., 2011). Climate model predictions suggest a seasonally sea ice-free Arctic well before the first half of this century (Overland and Wang, 2013; Docquier and Koenigk, 2021). The composition, structure and function of the Arctic microbiome will be altered with distinct effects on the marine system, on primary productivity, carbon fluxes and food web structures. Changes in the composition and structure of primary producers were already observed in Fram Strait (Nöthig et al., 2015), the boundary and highly dynamic zone between the Atlantic and the Arctic Ocean. These changes were reflected in the export flux of particulate organic matter (Lalande et al., 2013), also observable in the benthic communities (Jacob, 2014). Thus, understanding how the microbial communities changed over time under different environmental conditions is a scientific task needed to assess future changes in the Arctic ecosystem. This thesis aimed to understand the composition, distribution and function of bacteria, archaea and eukaryotic communities in Fram Strait across different spatial and temporal scales and their relationship with environmental variables. The overall objective was to identify signature groups and key factors of change, to provide a baseline to the effects of climate change and sea ice retreat. It provides a comprehensive overview of the Arctic microbiome by the incorporation of seawater, sinking particles and sea ice samples to identify key microbial indicators of change and environmental drivers in these communities. Samples were obtained in the frame work of the Long-Term Ecological Research (LTER) site HAUSGARTEN and the FRontiers in Marine Monitoring (FRAM) program. The results of Chapter I and Chapter II highlight the usage of methods free of compositional- bias and meta’omics approaches necessary to understand the role of microbial communities. The observations in Chapter I revealed that different water masses characterized by different physicochemical conditions harboured different active microbial communities. A late phytoplankton bloom dominated by diatoms in the surface waters of the eastern Fram Strait was identified, where members of the Bacteroidetes, Alteromonadales, Oceanospirillales and Rhodobacterales were significantly active. Abundant transcripts of transporters and fundamental cellular functions supported the degradation of organic matter. The deeper waters of Atlantic origin were marked by strong chemolithotrophic activities by members of Thaumarchaeota. In Chapter II I analysed bacterial and archaeal groups in deep-sea waters that benefitted from a phytoplankton bloom at the surface. Chapter III studied the development of microbial composition of sinking particles using a 12-year time-series study. The presence of sea ice and the passing warm anomaly were the drivers of change in these communities. In Chapter IV, microcosm experiments revealed bacterial taxa that responded to eukaryotes and substrates sourced from the sea ice during sea ice melt in seawater. Altogether, the results of this thesis provide baseline knowledge to better assess the effects of climate change on the Arctic microbiome and the consequences for ecosystem functioning and carbon cycling.