Discharge of Drinking Water Treatment Plants sludge directly on surface waters without any treatment is becoming an important issue in most countries around the world, behavior is not only affecting on the water quality, but also on soil and crops. This study investigated the effect of discharge of alum sludge and the variation in the level of the Nile water (flow regime) on water and soil qualities. The water samples were analyzed for physical, chemical and microbiological parameters. In winter (closure season), the mean values of EC, TDS, major ions, pH, DO and total algae count were higher than in summer. In summer (flooding season), it was noticed that the mean values of SiO2, metals, COD, BOD, TOC, nutrients and bacteriological parameters exceed winter season values. Moreover, the concentrations of Al, Fe, Mn were above WHO permissible limits and the concentrations of aggregate organic parameters exceed the FAO permissible limits in sites near the areas of sludge discharge. Most of water samples exceed the national guidelines. For soil, our findings showed that the concentrations of metals in soil samples collected from areas irrigated from canals receiving alum sludge are more (two-three times) than their concentrations from the pure sites. However, Pb concentration in the contaminated soil reaches ten times more than in the pure one. The management of sludge disposal becomes an urgent priority to save waterways, soil and crops from pollution. Finally, the variation in water flow during the winter closure period with reduction by ≈15 BCM is similar to the same reduction in the Nile flow when the Grand Ethiopian Renaissance Dam starts operation. This indicates that the long-term reduction in water flow due to the construction of this dam may cause serious environmental changes in the Nile River in Egypt.