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Zooplankton plays a key role in aquatic environments maintaining clear water conditions at low predation pressure via grazing on phytoplankton; thus, they can be sensitive indicators of environmental disturbances. According to climate predictions, arid and semi-arid regions will become warmer, and a critical consequence for lake ecosystems is salinization. Salinity, a critical abiotic factor influencing zooplankton survival, changes the trophic interactions in a lake. We explored the potential effects of conductivity (an indirect measure of salinity) on the zooplankton taxa in three lakes located in the Konya Closed Basin, Turkey. Zooplankton taxa show significant differences between lakes of low and high conductivity but do not display significant seasonal difference except Cladocera. Species diversity is shown to decrease with conductivity. Large-sized cladocerans such as Daphnia and Simocephalus appear in freshwater lakes; conversely, the halobiont Brachionus plicatilis was observed only in the brackish lake. Our results show that the changes in salinity will have a substantial impact on aquatic ecosystems.