Studies of annual successions and inter-annual variations in sub-Arctic and Arctic microplankton assemblages are required in order to understand the structure and function of marine ecosystems. This study depicts the microplankton (>20 μm) structure in a sub-Arctic tidewater glacial fjord system, SW Greenland. The descriptions are based on monthly net hauls collected between January 2006 and December 2010. Two blooms, with distinctive species compositions, were identified across all years: a spring bloom and a summer/autumn bloom. In addition, the winter season—with weak stratification, deep tidal mixing, and dense coastal inflows—was characterised by a separate species composition at much lower abundance. Here, the highest variety of microplankton groups was recorded and represented by diatoms (Chaetoceros spp. and Thalassiosira spp.), silicoflagellates, dinoflagellates, and ciliates. During the spring bloom, species correlated with higher light intensities, i.e. haptophytes and diatoms (Thalassiosira spp. and Fragilariopsis spp.), dominated the microplankton assemblage. Among these, diatoms were also correlated with cooler and fresher waters influenced by springtime melt. During the summer/autumn bloom, the microplankton assemblage was mainly represented by diatoms, such as Chaetoceros spp. ‘Low-saline’ chrysophytes were also present. The latter bloom coincides with elevated temperatures in the fjord and renewal of nutrients due to the onset of glacial meltwater run-off from the Greenland Ice Sheet. Our study shows a yearly recurrent succession of microplankton assemblages and that the annual succession is controlled primarily by ocean-fjord-glacier interactions.