To evaluate the effects of meltwater discharge from marine-terminating glaciers on a fjord protist community in northwestern Greenland during summer, we investigated the distribution, abundance and biomass of the protist community and their relationships with hydrographic parameters. In the standing stock of protists, dinoflagellates (46.4%) and oligotrich ciliates (39.5%) were dominant throughout the study region. With respect to vertical distribution, oligotrich ciliates were abundant in the surface layer, mainly due to suitable food conditions (abundance of diatom and nanoflagellates). Near glaciers, relatively high chlorophylla(chla) concentrations were found in the subsurface layers associated with the low-temperature, high-turbidity and slightly high nutrient levels, indicating that the nutrient inputs from the upwelling glacial meltwater plume increased primary production. Large-sizedProtoperidiumspp. were found only at stations near glaciers where nutrients were abundant, and heterotrophic dinoflagellates showed strong relationships with nanoflagellates. These findings suggest that the upwelling associated with subglacial meltwater discharge can stimulate nanoflagellate production, resulting in increases in ciliate and heterotrophic dinoflagellate production.