Planktivorous fish can exert strong top-down control on zooplankton communities. By incorporating different feeding strategies, from selective particulate feeding to cruising filter feeding, fish species target distinct prey. In this study, we investigated the effects of two species with different feeding strategies, the three-spined stickleback (Gasterosteus aculeatus (L.)) and roach (Rutilus rutilus (L.)), on a low-diversity brackish water zooplankton community using a 16-day mesocosm experiment. The experiment was conducted on a small-bodied spring zooplankton community in high-nutrient conditions, as well as a large-bodied summer community in low-nutrient conditions. Effects were highly dependent on the initial zooplankton community structure and hence seasonal variation. In a small-bodied community with high predation pressure and no dispersal or migration, the selective particulate-feeding stickleback depleted the zooplankton community and decreased its diversity more radically than the cruising filter-feeding roach. Cladocerans rather than copepods were efficiently removed by predation, and their removal caused altered patterns in rotifer abundance. In a large-bodied summer community with initial high taxonomic and functional diversity, predation pressure was lower and resource availability was high for omnivorous crustaceans preying on other zooplankton. In this community, predation maintained diversity, regardless of predator species. During both experimental periods, predation influenced the competitive relationship between the dominant calanoid copepods, and altered species composition and size structure of the zooplankton community. Changes also occurred to an extent at the level of nontarget prey, such as microzooplankton and rotifers, emphasizing the importance of subtle predation effects. We discuss our results in the context of the adaptive foraging mechanism and relate them to the natural littoral community.