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The present study aimed to evaluate the diversity of zooplankton including rotifers and cyclops in the various freshwater ecosystems in Assiut Governorate, Egypt. Rotifers can affect the prevalence of different protozoan organisms in water, such as Cryptosporidium species. Cyclops act as intermediate host of some helminthic parasites. Microscopic analysis of the collected samples identified 3 rotifer genera and one copepod in different freshwater supplies including poultry farms, animal farms, human tanks, and fish farms. In the present study, 59 out of 136 (43.3%) water samples were contaminated with plankton. Poultry freshwater showed the highest plankton diversity and prevalence with 29 samples (21.3%), whereas the least prevalence was in human drinking water, 3 (2.2%). In the fishpond, Cyclops were observed in 3 (2.2%) of total samples. The prevalence of rotifers and Cyclops is strongly related to the summer season. Our results enrich the diversity of zooplankton in different freshwater supplies as a bioindicator of water pollution. [ABSTRACT FROM AUTHOR]