The present study investigated the effect of environmental variables on the abundance and distribution of zooplankton in different habitats along the Nile River in Shattura Village. Zooplankton samples were collected from three distinct sites along the Nile River in Shattura Village, each exhibiting different environmental characteristics: Site 1 with vegetation, site 2 lacking vegetation, and site 3 being a drain canal. The study spanned from spring 2020 to winter 2021, during which the physico-chemical parameters of the water were analyzed. Rotifera constituted the majority of the zooplankton (54.73%), followed by Cladocera (20.59%), Copepoda (13.1%), and Ostracoda (8.9%). Among the 52 identified zooplankton species, Rotifera comprised 18 species, Cladocera 13 species, Copepoda 10 species, and Ostracoda 11 species. Site 1 exhibited the highest zooplankton density (44.08%), attributed to the presence of vegetation, followed by site 3 (37.18%), influenced by agricultural drains, and site 2 had the lowest density (18.73%). Zooplankton abundance peaked in summer and declined in winter. Notably, Rotifera abundance increased in populated sites (site 3), whereas other zooplankton groups thrived in less populated areas. Correlation analyses revealed positive associations between Rotifera and Cladocera with electric conductivity, total dissolved solids (TDS), chloride (Cl), calcium (Ca), and sulfate (SO4). Conversely, Copepoda showed positive correlations with water transparency, pH, dissolved oxygen, and biological oxygen demand (BOD). Overall, seasonal variations significantly impacted the zooplankton community, with Rotifera dominating and Ostracoda being the least abundant. High values of the Shannon–Weaver diversity index, richness, and evenness suggested ample food resources and favorable growth conditions. Transparency, conductivity, pH, dissolved oxygen, and BOD were identified as the key influencing parameters on zooplankton abundance. Additionally, vegetation and agricultural drains strongly influenced total zooplankton levels.