The New Urban Communities Authority (NUCA) has allocated EGP 17.5 billion for the initial development of El-Warrak Island, encompassing green spaces, utilities, roads, residential units, and resident compensation. Thus, this research investigated the interplay between natural and anthropogenic factors due to the development affecting zooplankton dynamics to maintain ecological equilibrium and uphold species diversity. Four stations were strategically selected to represent all habitats surrounding El-Warrak Island. Findings revealed consistent water temperatures with minimal fluctuations, stable pH values with slight seasonal variations, and minor spatial and seasonal changes in EC and TDS values. The zooplankton community in the River Nile consisted of Rotifera, Protozoa, Copepoda, Cladocera, and free-living Nematoda, with an average total density of 595,297 ind. m-3. Notably, Rotifera constituted the majority, representing 91.48% of the total zooplankton density. Station 1 exhibited the lowest zooplankton density, while Station 4 recorded the highest population density, averaging 198,868 and 950,574 ind. m-3, respectively. Population density peaked in the cold season and decreased to its lowest level in the hot season. Thirteen distinct rotifer species were identified, with Keratella cochlearis being the most populous. The diversity index (H`) revealed that Station 1 exhibited the highest diversity (H' = 2.2). Moreover, the saprobic index values for stations 1, 2, 3, and 4 were determined to be 1.8, 1.7, 1.7, and 1.7, respectively, indicating a β-mesosaprobic condition at the investigated sites. In conclusion, intensive agricultural and domestic activities have been identified as significant contributors to high organic pollutant levels, impacting ecological health, and diminishing zooplankton species diversity. Therefore, effective mitigation and treatment methods should be implemented.