In Arctic coastal regions, the phytoplankton bloom is often initiated by meltwater induced stratification in spring, while subsequent nutrient depletion is believed to drive phytoplankton succession in summer. The associated changes in photophysiology are difficult to identify, because these can be governed by acclimation to light and nutrient availability as well as variations in phytoplankton biomass and taxonomic composition. In the present study, the consequences of nutrient limitation for photophysiology and growth were assessed in natural phytoplankton communities from Kongsfjorden, Spitsbergen. A series of nutrient addition experiments demonstrated N‐limitation from mid‐June onwards and possible co‐limitation with P later in summer. The onset of N‐limitation was associated with a pronounced change in taxonomic composition from a dictyochophytes to a haptophytes dominated community. Fast Repetition Rate fluorometry measurements of photosystem II (PSII) photophysiology showed that the dictyochophytes dominated community was characterized by high PSII efficiency and electron transport rates which were efficiently used for growth. Marked changes in PSII photophysiology were observed later in summer, with decreasing efficiencies, lower connectivity between reaction centers, and slower turnover rates. Simultaneously, alternative electron requirements downstream of PSII became more important and energy was likely allocated to the uptake of nutrients rather than carbon fixation and growth. Relief of nutrient limitation during the nutrient addition experiments did not lead to pronounced changes in PSII photophysiology. It is, therefore, concluded that PSII photophysiology of the phytoplankton community in Kongsfjorden is associated with changes in species composition rather than a direct effect of nutrient availability or nutrient limitation.