In the present study, the diversity and seasonal variation of the freshwater zooplankton were studied throughout a period of one year (September 2020 to August 2021). Sampling collections were monthly carried out from fifteen sites representing 7 cities located north, and south to Qena city from the River Nile and its branches (26°9'18.22"N and a longitude of 32°42'57.64"E). Physiochemical factors of water of the different collecting sites were measured and analysed using One-way Analysis of variance (ANOVA), and 195056 individuals were collected. Shannon-Weiner diversity, Equitability and Margalef's indices were used to determine zooplankton composition. The results revealed that there were 48 taxonomic units dominated by cladocerans (87%, 23 taxa) followed by copepods (11.74%, 12 taxa), rotifers (1.01%, 8 taxa), and ostracods (0.24%, 3 taxa). The most common species of Cladocera was Chydorus sphaericus representing 62.95 %; while the most common of Copepoda was Messocyclops ogunnus representing 34.71%. The most common species of Rotifera was Lecane lune representing 34.80 %; whereas, the most common of Ostracoda was Cypridopsis vidua representing 96.22 %. Both zooplankton communities and populations of Cladocera showed higher density during the rainy season. Investigation on the physiochemical parameters showed that pH, turbidity, and dissolved oxygen all recorded maximum values in the autumn season. Furthermore, both the total dissolved solids and conductivity recorded maximum values in the winter season. Total abundance of zooplankton showed a positive relationship with Taxa richness, Shannon-Weiner diversity, and Margalef's index and Equitability. They showed their peaks during the winter season, while the evenness index increased in the dry season.