The biological carbon pump removes CO2 from the atmosphere via phytoplankton growth in the sunlit stratified upper ocean. This is followed by a partial export to deeper water layers and finally deposition on the sea floor. In polar regions, sea ice affects stratification and light availability. However, it remains unclear to what extent sea ice cover affects the biological carbon pump. Additionally, climate change is expected to increase the seasonal ice zone (i.e., the part of the ocean that is ice-covered for part of the year). Observational time series of the seasonal cycle contrasting production and export in ice-covered and ice-free conditions are still scarce. Here, we present multidisciplinary time series observations from the marginal ice zone in Fram Strait (located between Greenland and Svalbard) of all ocean compartments from the sea surface to the seafloor. Data are from two contrasting years when our measurement site was either partially ice-covered (2016-2017) or when the ice edge was located further to the north (2017-2018). We start by introducing the study site followed by a description of the atmospheric forcing and its effects on the upper ocean stratification and hydrography. In mostly ice-free conditions, the mixed layer went from deep to stratified in a single event, whereas the presence of sea ice resulted in a number of alternating events of shallow and deep mixed layers. These patterns changed phytoplankton and bacterial dynamics and upper ocean chemistry. The onset of the bloom was much more gradual in the presence of sea ice. We also explore the different trophic levels in the upper that contributed to the export recorded at the seafloor which fueled biological benthic activity a few weeks after the bloom. Our observations reveal an impact of the respective sea ice patterns on concomitant species and biogeochemical reactions in the upper water column and for the export of organic matter to the deep sea in the Fram Strait.