Mysid shrimp (Mysis diluviana) were introduced to Lake Tahoe in the mid-1960s to supplement the diets of non-native salmonids. By the mid-1970s, the introduction had caused a decline in the abundance of kokanee salmon (Oncorhynchus nerka) and a loss of native cladocerans (Daphnia spp. and Bosmina longirostris) from the pelagic zone. Recently, management of the lake’s mysid population has been suggested as a means to improve the lake’s clarity. This warranted an investigation to determine the roles of different zooplankton taxa in controlling the pelagic processes linked to water clarity. Laboratory mesocosm experiments were conducted to determine the effects of Daphnia spp., a native copepod (Epischura nevadensis), the non-native mysid, and a community of these organisms on oligotrophic Lake Tahoe and its mesotrophic embayment, Emerald Bay. A 64% decrease in algal biovolume was observed in Emerald Bay water incubated with Daphnia. Decreases of 53%, 23%, and 46% in concentrations of small particles were observed in Emerald Bay water incubated with Daphnia, juvenile mysids, and the community, respectively. A 46% decrease in large particles was observed in Lake Tahoe water incubated with juvenile mysids, and a 44% decrease in large particles was observed in Emerald Bay water incubated with Daphnia spp. Dissolved organic carbon concentrations decreased by 25% in Lake Tahoe water incubated with Daphnia and by 26% in water incubated with adult mysids. This study further elucidates the effects that these zooplankton have on the Lake Tahoe and Emerald Bay ecosystems beyond just the fish populations.