The River  Nile is the essence of life in Egypt; the last decades have witnessed changes in its water quality due to several factors associated with anthropogenic activities. Therefore, the aim of this study was to evaluate the ecological status of the River Nile at the Rosetta branch by addressing the relationship of plankton densities and heavy metals. 99 species of phytoplankton were recorded belonging to 6 major groups, with the dominance of diatoms. While, 39 species of zooplankton were recorded belonging to 4 major groups, with the dominance of Rotifera. The concentration of heavy metals in the surface layer of the study areas varies with the season and site with the prevalence of Al, followed by Fe, Mn, Zn, Ni, Co, and Cd. Pearson's correlation and redundancy analysis showed that the concentrations of these metals are correlated with the abundance of selected dominant phytoplankton and zooplankton species. In addition, Van Dobben circles analysis elucidated that heavy metals are significantly contributed to the species richness and distribution. Thus, it is recommended to establish sewage water treatment plants in the Rosetta branch before draining into the Nile.