Over the last decades, the western Arctic Ocean has undergone unprecedented environmental changes. However, long-term in situ observations of marine phytoplankton are still rare and therefore insufficient to fully characterize their evolutionary trends. This study investigated the diatom fluxes and composition in sediment trap material collected from the Northwind Ridge, western Arctic Ocean, from August 2008 to September 2009. Our data showed that Chaetoceros resting spores were the predominant species, accounting for >40% of the diatom composition. The sea ice diatom group, which included Fossula arctica, Fragilariopsis cylindrus and F. oceanica, dominated the rest of the assemblage throughout the observation period. While diatom fluxes in winter were extremely low, higher flux values were found in summer, and summer 2009 flux values were twice as high as those in 2008. The high total mass and diatom fluxes in summer 2009 were attributed to the combined effect of a weakened Beaufort Gyre, a strengthened Pacific water inflow (PWI) and the distribution pattern of the sea ice. The higher levels of coastal diatoms and terrigenous proxies in summer 2009 were consistent with the intensified PWI. Sea ice diatoms and sea ice biomarker IP25 fluxes were both high during the sea ice melting season and were significantly correlated with each other (r² = 0.64, p < 0.01). Our data also suggest that sea ice diatoms are prone to selective dissolution in the water column and sediments, implying the existence of biases in diatom assemblage data and subsequently in paleoceanographic reconstructions.