Herbivorous zooplankton may have a pronounced influence on pelagic microorganisms in Arctic freshwaters. We quantified experimentally the size-selective feeding of several zooplankton groups on pelagic microorganisms in high Arctic tundra systems. Our experiments and field study focused on dominant herbivores in Arctic freshwaters, including the cladoceran Daphnia, the copepod Diaptomus and the anostracan Branchinecta, and their effects on prey ranging in size from bacteria to large phytoplankton. Grazing experiments showed that Daphnia were effective predators on all types of prey, whereas Diaptomus grazed preferentially on larger phytoplankton with low clearance rates for bacterial cells. Further analysis by flow cytometry indicated that Diaptomus grazed selectively on the largest bacteria. In contrast to the results obtained in the controlled experiments, Arctic lakes and ponds with a zooplankton community dominated by Daphnia had a higher bacterial production and abundance than systems not dominated by this grazer. This may indicate that the stimulatory effect of grazers on bacterial growth is more pronounced in natural systems, or that factors other than zooplankton grazing are more important in regulating bacterial abundance and production in natural systems. Although Arctic waters differ considerably from temperate systems with respect to temperature and light regime, herbivore–prey dynamics as well as the bacterial response to temperature appear to be similar between the climatic regions.