<jats:title>Abstract</jats:title> <jats:p>Repeated measurements of benthic and pelagic parameters in the rapidly changing Arctic Ocean provide a unique insight into spatial and interannual trends and changes in the ecosystem. Here, we compiled biogenic and biogeochemical measurements collected from sediment cores at the Long-Term Ecological Research Observatory HAUSGARTEN located in the Fram Strait. A total of 21 stations were visited yearly over a period of 18 years (2002–2019). The time series highlighted an increase in bacterial numbers for samples collected 50 days after the peak phytoplankton bloom. Although bacterial abundances were not bathymetric depth-dependent when viewed across all years, we observed a seasonal trend in benthic microbial abundance closely related to the timing of the phytoplankton bloom with a time-lag of 100 days between the surface phytoplankton peak and the peak in bacterial abundance in the sediment. Considering the residence time of phytoplankton in the upper ocean and the water depth, we estimated an average settling velocity for phytodetritus of 30 m.d−1, which is similar to previous observations from Fram Strait. This suggests that settling organic matter promotes vertical microbial connectivity and benthic bacterial abundance in the deep ocean, shaping the microbial biogeography, diversity, and biogeochemical processes.</jats:p>