Time-series observations provide an essential baseline to identify biological responses to environmental fluctuations, and to distinguish natural variability from human impact. Here, we describe for the first time year-round microbial and oceanographic dynamics in the partially ice-covered Fram Strait (Arctic Ocean) using autonomous samplers deployed as part of the infrastructure program FRAM, allowing unprecedented insights into the marine microbial ecology of the polar night. Bacterial communities showed a strong seasonal signal, especially in the West Spitsbergen Current. Here, distinct temporal succession of phytoplankton and bacterial clades occurred, including covariance of the magnetotactic bacterium Magnetospira with daylight hours. Summer featured weekly variability in blooming taxa, including the flavobacterial genera Formosa and Polaribacter succeeding peaks of the diatoms Thalassiosira and Grammonema. The Bacteroidetes peak in summer was followed by dominance of SAR11 in fall and Nitrosopumilus in winter, suggesting timely controlled ecological roles. Bacterial diversity was highest in winter, featuring elevated abundances of Planctomycetes and Nitrospinia as well as the heterotrophic eukaryote taxa Syndiniales and Radiolaria. Late winter was characterized by increasing proportions of e.g. Dadabacteria before the onset of the productive season. In the ice-covered East Greenland Current (Arctic Ocean outflow), bacterial community structure showed less seasonality. Here, bacterial diversity decreased in response to ice cover dynamics and nitrate availability, underlining that changing ice and light regimes likely impact plankton diversity and biogeochemical processes.