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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 aand 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.

Effects of prolonged darkness on Arctic phytoplankton composition were investigated with lab experiments and a pigment time series in Kongsfjorden, Spitsbergen (78°55′N). Chlorophyll a(Chl a), pigment composition, particulate organic carbon, cell numbers, and photosynthetic characteristics were studied in Arctic diatoms (Thalassiosira antarctica, Thalassiosira nordenskioeldii) and flagellates (Rhodomonassp., Micromonassp.) during 8 weeks of darkness and subsequent recovery in irradiance. Loss of photosynthetic functionality after 2 weeks of darkness was reversible in all species when returned to irradiance. Diatoms were more resistant to prolonged darkness (> 2 weeks) compared to the flagellates, with lower decline rates of Chl aand maximum quantum yield of PSII. T. nordenskioeldiishowed rapid growth during recovery throughout 8 weeks of dark incubation, whereas recovery of flagellates diminished within 4 weeks. Ratios of taxonomic marker pigments relative to Chl aof all species showed limited variation during 8 weeks of dark incubation. The experimentally observed enhanced dark survival of diatoms was in agreement with pigment observations during four polar nights (2013–2017) in Kongsfjorden, which showed increased relative diatom abundance during declining biomass (down to 0.02 mg Chl am−3). Therefore, a period of prolonged darkness gives Arctic diatoms a head start during the early stages of the spring bloom. The taxon‐specific survival traits can influence the geographical distribution of diatoms and flagellates within the polar oceans and their phenology. Furthermore, the persistence of Chl aof nonviable phytoplankton during darkness might influence biomass estimates during the polar night.