Zooplankton is an important bio-indicator of ecosystem integrity. The present study aimed to evaluate the zooplankton community and measure some physical and chemical characteristics of the water, during the period from September 2020 to August 2021. Samples were collected from 15 sites located in the River Nile and its tributaries (26°9'18.22"N and 32°42'57.64"E) at Qena Governorate. Eleven representatives of water samples were collected to measure physico-chemical parameters, including temperature, pH, total dissolved solids, conductivity, turbidity, dissolved oxygen and some heavy metals (manganese, copper, zinc, chrome and cobalt). Investigation of the physio-chemical parameters showed that pH, turbidity, dissolved oxygen, total dissolved solids, and conductivity recorded maximum values in winter. Heavy metals such as cobalt (Co) recorded the highest concentration in winter and the lowest in autumn. Chromium (Cr) recorded the highest concentration in autumn and the lowest in spring. Manganese (Mn) recorded the highest concentration in spring and the lowest in autumn. Copper (Cu) and zinc (Zn) concentrations reached their highest in summer and lowest in autumn. On the other hand, Cladocera and Copepoda were the most dominant populations, which were negatively correlated with water temperature (r=-0.474) and (r=-0.118), respectively. While, they were positively correlated with total dissolved solids, conductivity, turbidity and cobalt.