The aim of this study was to identify differences between different types of water body within the same river basin by comparing the composition of the zooplankton community. The study was conducted in three types of water body in the Sakarya Basin in northwestern Turkey: an alluvial barrier lake (Lake Poyrazlar), a pond (Sorgun Pond), and a reservoir (Çubuk II Reservoir). The spatiotemporal changes of these three types of aquatic habitats were investigated in terms of the zooplankton organisms by examining their diversity, evenness, and differences in the abundance of species. A total of 81 species were identified. Thirty-eight species were observed in one water body only, while 15 species were observed in all the water bodies. Two of the 15 species belonged to the group Cladocera, while the rest belonged to the phylum Rotifera. The water bodies were different in terms of all the zooplankton species and cladocerans, even though they were located within the same basin. In addition, the size of the lake area and its electrical conductivity may affect species diversity and richness depending on the amount and quality of water inflow.