Water and sediment samples were collected from six different stations, located along the Nil River between February and June 2015. Concentrations of cadmium, lead, zinc, and copper were determined. The extent of the sediment pollution was assessed, using the multiple pollution indices, namely contamination factor (CF), pollution load index (PLI), and the geoaccumulation index (Igeo). The results showed that the level of metals in water samples exceeded background concentrations for Cd and Pb, and the average values for those elements were higher than those of Zn and Cu, ranked as the following: Pb (0.58)> Zn (0.38)> Cd (0.32)> Cu (0.061). For sedimentary samples, the results showed that Zn and Pb concentrations were greater than the concentrations of Cu and Cd, exceeding the background values (except for Cu). The concentration of the tested heavy metals decreased to the following order: Zn (96.2)> Pb (61.5)> Cu (38.83)> Cd (2.34). The Igeo values revealed that Cd (2.87) and Pb (1.61) had accumulated significantly in the Nil River. Contamination factor (CF) confirmed that the sedimentary samples were moderate to very high in terms of Cd, Pb, and Zn contamination. The Pollution Load Index (PLI) values were above one (>1), indicating an advanced decline of the sediment quality. Also, the results showed that the stations, located at the middle portion of the river (S3, S4, and S5) have higher levels of metals than the other stations (S1, S2, and S6). The assessment of heavy metals' levels in water and sedimentary samples indicated that river water and the sediments in the study area were strongly impacted by agricultural activities and domestic waste water.