Fjords on the west coast of Spitsbergen experience variable Arctic and Atlantic climate signals that drive seasonal and inter-annual variability of phytoplankton productivity and composition, by mechanisms that are not fully resolved. To this end, a time series (2013–2018) of Kongsfjorden (N 78°54.2, E 11°54.0) phytoplankton pigments, ocean physics, nutrient concentrations, and microbial abundances was investigated. Kongsfjorden phytoplankton dynamics were predominantly governed by solar radiation and cycles of warming and freshwater discharge that caused pronounced changes in light and nutrient availability. Phytoplankton growth after the polar night commenced in March in a mixed, nutrient loaded water column, and accelerated in April after weak thermal stratification. Spring (weeks 10–22) showed high diatom relative abundance that ceased when silicic acid and nitrate reached limiting concentrations. Summer (weeks 23–35) was characterized by sixfold stronger stratification due to increased freshwater discharge and continued ocean heating. This caused a warm, low salinity surface layer with low nutrient concentrations. Small and diverse flagellates, together with high bacterial and viral abundances, thrived in this regenerative, N or P-limited system. Elevated late summer chlorophyll a (Chl a), and ammonium suggested increased regeneration and nutrient pulses by glacial upwelling. Fall (weeks 36–48) caused rapidly declining Chl a and increasing diatom relative abundance, which persisted throughout the polar night, causing high diatom relative abundance during spring. Despite inter-annual variability in ocean temperature and salinity we observed relatively stable seasonal phytoplankton taxonomic composition and Chl a.