The disposal of El-Sail drain, Kom Ombo drain, Edfu ferroalloys factory, and Edfu sugar cane factory around Aswan city poses a serious threat to the River Nile waters, especially El-Sail and Kom Ombo drains which recorded higher microbial load. Kom Ombo drain recorded higher total bacterial counts (TBC) at 22 ºC (1800 x10³ cfu/ml), thermophilic bacteria (259 cfu/ml) and spore-forming bacteria (15.8 x10³ cfu/ml). While El-Sail drain recorded higher TBC at 37 ^oC (137 x10³ cfu/ml) and higher values for indicator bacteria (total coliforms, faecal coliforms, and faecal streptococci). In addition, warmer seasons (spring and summer) showed higher counts of indicator bacteria Salmonella sp. and Shigella sp. in 22 and 30 % of samples, respectively, whereas Escherichia coli was detected in all sites, recording the highest values at El-Sail drain samples. Furthermore, El-Sail drain samples recorded the highest values for electrical conductivity, total dissolved solids, biochemical oxygen demand, NH₃, NO₂^- and PO₄^3-, while Kom Ombo drain samples recorded the highest values for water temperature and NO₃^-. Ranks of water quality index (WQI) were good in all sites, except for the disposal sites which ranged from fair to marginal. In conclusion, the River Nile water at Aswan governorate is heavily polluted, especially at El-Sail drain and Kom Ombo drain. Consequently, treatment and safe disposal of different industrial and domestic wastes are recommended.