Arctic fjords are coastal ecosystems whose productivity is strongly impacted by glacial meltwater. Fjords affected by marine-terminating glaciers (MTGs) sustain highly productive, diatom-dominated blooms throughout the growing season, whereas fjords with land-terminating glaciers (LTGs) typically experience a diatom spring bloom followed by less productive, small-celled communities in summer. However, the biomass, community composition and size structure of these phytoplankton communities, particularly pico- and nano-sized components, remain underexplored. We investigated spring–summer contrasts in the phytoplankton of two adjacent SW Greenland fjords: Nuup Kangerlua, mainly impacted by MTGs, and Ameralik, impacted only by an LTG. Combining high-throughput imaging, pigment and metabarcoding approaches allowed us to resolve the functional (size, pigmentation) and taxonomic composition of the phytoplankton communities. Our analyses revealed seasonal divergence between the two fjords. In spring, both were dominated by colony-forming diatoms under nutrient-replete conditions. In summer, nanophytoplankton dominated both fjords. However, persistent subglacial upwelling sustained growth of non-colonial diatoms in the MTG fjord, whereas pico- and nano-sized chlorophytes and cryptophytes dominated the warmer, less saline, turbid and highly stratified surface waters of the LTG fjord. Increased importance of mixotrophy under these conditions suggests an efficient microbial loop, partly relying on regenerated nitrogen. In contrast, the inner MTG fjord was characterized by the harmful haptophyte <em>Pseudohaptolina birgeri</em>. Despite these compositional differences, phytoplankton biomass and primary production remained similar between fjords. Overall, our results suggest that continued glacial melt and retreat of MTGs onto land will alter phytoplankton community organization, with cascading effects on Arctic food webs and carbon cycling.