Arctic phytoplankton are highly sensitive to seawater physical and chemical conditions, especially in the context of rapid climate change and sea ice loss. We studied the spatial and seasonal distributions of diatoms, dinoflagellates and coccolithophores, and clarified their associations with light, temperature and nutrients in the western Barents Sea in late summer 2017, and winter, spring and early summer 2018. Diatoms, composed mainly of Chaetoceros, Fragilariopsis and Thalassiosira, bloomed in spring at the southern border of the marginal ice zone with mean abundance of 1.1 × 106 cells L−1 and biomass of 119.5 µg C L−1, and were observed to follow the retreat of sea ice in the Arctic water to the north at the shelf break near Nansen Basin, contributing to the progression of the summer situation. Dinoflagellates flourished in surface waters south of Svalbard in summer, with maxima of 2.2 × 105 cells L−1 and 78.2 µg C L−1. High abundances and calcite mass of coccolithophores were detected in the southern Barents Sea and southwest of Svalbard in summer, with maxima of 3.3 × 105 cells L−1 and 4.7 µg C L−1. Two distinct phytoplankton assemblages, closely linked with Atlantic water and Arctic water, were geographically separated by the Polar Front in two summers, with a percent similarity below 11.9%, suggesting great influence of the two water masses on large-scale distributions of phytoplankton. Redundancy analysis revealed that temperature was one of the most important factors in shaping the seasonal distributions of diatoms, while irradiance showed positive correlation with dominant dinoflagellates of each season. From the perspectives of phytoplankton composition and carbon biomass, our findings highlight the governing effect of physical seawater conditions on driving seasonal patterns of phytoplankton biogeography, as well as the pivotal role of nutrients in supporting the phytoplankton growing seasons in the western Barents Sea.