This paper presents the diatom and palynomorph data from a sediment trap deployed in the northern part of the East Barents Sea for an annual cycle from August 2017 to August 2018. The average monthly fluxes of diatoms and dinoflagellate cysts in the photic layer of the northeastern part of the Barents Sea varies from 10.4 × 103 to 640.8 × 103 valves m−2 day−1 and from 0.3 × 103 to 90.0 × 103 cysts m−2 day−1, respectively. Their fluxes are related to the low irradiance of the photic layer during the sea-ice cover period, dominance of southward currents, modern climate, and nepheloid layer conditions. Based on redundancy analysis of the relationship between the fluxes of diatoms and dinoflagellate cysts and organic carbon fluxes, sea-ice covers, and the seasonal cycle of light availability we determined the following. First, sea-ice-associated diatoms and dinocysts are exported to the sediment trap from the melting sea ice with a two-week delay. Second, the appearance of freshwater diatoms and green algae in the sinking material accumulating from March 2018 to July 2018 is also related to the melting of sea ice. And third, the presence of Coscinodiscus radiatus, C. perforatus, Shionodiscus oestrupii and Operculodinium centrocarpum in the diatoms and dinocysts species composition throughout the year indicates the advection of Atlantic waters into the Barents Sea up to 80° N.