A relationship between chemical pollution and its harmful effects on zooplanktons has been established. So, changes in composition and population numbers of them in different sites of Bahr Shebeen Nilotic canal, in relation to environmental factors, metals and pesticides concentrations were investigated in the present study. Ecological parameters showed fluctuations in values during the successive months from September, 2014 to August, 2015. Shannon diversity index was the highest at site 2 followed by sites 3 and 1. Sites were significantly different in metals concentrations as Fe, Pb and Al, and pesticides residues as organophosphorous and organochlorine. In conclusion, zooplankton populations were preferred by specific taxa in the selected sites because of the change e of pollutant type especially in density and appearance/disappearance of some phyla leading to variability in zooplankton diversity.