Samples of water, sediment and two native plants (Eichhornia crassipes and Ceratophyllum demersum), collected seasonally from eight sites, were analyzed to investigate the level of contamination with metals (Fe, Mn, Ni, Co, Zn, Cu, Cr, Pb and Cd) in the Nile River in the Cairo region, using heavy metal pollution and contamination indices in the case of water, and the geoaccumulation index, the pollution load index, the enrichment factor and the potential ecological risk factor in the case of sediment. The results clarified that the levels of metals among three compartments were in order: sediments > plants > water. The Nile water in Cairo is not critically polluted by the studied metals and the metal pollution index for most sites does not exceed the critical limit (< 100). Sediment samples showed a clear accumulation of Mn, Ni and Cd when compared with benchmarks cited by the Environmental Protection Agency (EPA), especially during low flow seasons. The contribution of Cd to the ecological risk assessment was about 80%, while the contribution of Ni was about 10%, reflecting that these elements originated primarily from anthropogenic sources. Eichhornia crassipes and Ceratophyllum demersum have a higher accumulation capacity for Mn, Cu and Fe compared to the other studied metals.