Six cruises to the polluted areas of Rosetta branch were carried out from January 2003 to November 2003 on bimonthly basis. Raw sewage from El-Rahawy drain and industrial effluents from Kafr El-Zaiyat factories represent the highly polluted area along Rosetta Nile branch. Dissolved oxygen was completely depleted at discharging area of raw sewage. Total organic nitrogen at two wastes was higher than inorganic forms. Ammonium concentrations loaded with raw sewage (2.87 mg/L) were much higher than that recorded in effluents of Kafr El-Zaiyat factories and exceed the maximum acceptable concentration (0.1 mg/L). Also, total organic phosphorus at the mixing areas of the two wastes increased than the upstream stations. Trace metal concentrations loaded with industrial effluents were distinctly high compared to domestic sewage either water or sediment. Phytoplankton communities at the discharging point of raw sewage and industrial waste showed an obvious decline compared to upstream and downstream stations. Bacillariophyceae dominated upstream of El-Rahawy stations, Chlorophyceae dominated downstream, while Cyanophyceae dominated mixing area. On the other hand, Chlorophyceae dominated at all stations of Kafr El-Zaiyat. This study aimed to avoiding discharge of raw sewage and industrial wastes into River Nile after explaining their hazardous impact on aquatic environment.