Lake Nasser is assumed to be the largest man-made lake in northern Sudan and southern Egypt. It has paramount importance to Egypt as it supplies water to the country. That's why the lake's water quality must be continuously monitored to cope with the difficulties of water scarcity and a reliable water supply. Thus, in March and July 2019, fifteen sites were chosen to reflect the various habitats of the whole lake.  Twenty-one adult zooplankton species were found, belonging to Rotifera, Cladocera, and Copepoda with a total density of 16945 org. m^-3. Copepoda emerged as the dominant constituent of the community both before and during the flood seasons.  The zooplankton Shannon Weaver index value was at its highest in the western sector of Tushka (H`= 2.46), while the eastern sector of Aswan station had the lowest value of biodiversity (H`= 1.97). Macrobenthic fauna consisted of 9 species represented by three phyla; Annelida, Arthropoda, and Mollusca with a percentage of 74.62%, 15.41%, and 9.97%, respectively and the total density was 863 org. m^-2 where the highest densities were found in the southern sectors of the lake. The western station of EL Madiq sector revealed the highest benthic Shannon Weaver index (H′= 1.55) which could be ascribed to the preponderance of 4 species of arthropods and exclusively prevalence of nymphs of Ischneura. Contrary, the middle stations of Wadi Abyad and Aswan sectors recorded the least diversity Shannon Weaver values (H′= 0.21 and 0.27, respectively). The present study revealed that the number of macrobenthic species decreased dramatically to 9 compared to 15, 43, 39, and 24 in 1987, 1993, 1995, and 2013, respectively. It is recommended to force an effective legal framework to mitigate pollution in Lake Nasser.