The concentrations of Cd, Cu, Pb, and Zn in sediments, water, and different plant organs of six aquatic vascular plant species, Ceratophyllum demersum L. Echinochloa pyramidalis (Lam.) Hitchc. & Chase; Eichhornia crassipes (Mart.) Solms-Laub; Myriophyllum spicatum L.; Phragmites australis (Cav.) Trin. ex Steud; and Typha domingensis (Pers.) Poir. ex Steud, growing naturally in the Nile system (Sohag Governorate), were investigated. The aim was to define which species and which plant organs exhibit the greatest accumulation and evaluate whether these species could be usefully employed in biomonitoring and phytoremediation programs. The recorded metals in water samples were above the standard levels of both US Environmental Protection Agency and Egyptian Environmental Affairs Agency except for Pb. The concentrations of heavy metals in water, sediments, and plants possess the same trend: Zn > Cu > Pb > Cd which reflects the biomonitoring potentialities of the investigated plant species. Generally, the variation of heavy element concentrations in water and sediments in relation to site and season, as assessed by two-way repeated measured ANOVA, was significant (p < 0.05). However, insignificant variations were observed in the concentrations of Pb and Cd in sediments in relation to season and of Cu and Zn in relation to site. Results also showed that the selectivity of the heavy elements for the investigated plants varied significantly (p < 0.05) with species variation. The accumulation capability of the investigated species could be arranged according to this pattern: C. demersum > E. crassipes > M. spicatum > E. pyramidalis > T. domingensis > P. australis. On the basis of the element concentrations, roots of all the studied species contain higher concentrations of Cu and Zn than shoots while leaves usually acquire the highest concentrations of Pb. Cd concentrations among different plant organs are comparable except in M. spicatum where the highest Cd concentrations were recorded in the leaves. Our results also demonstrated that all the studied species can accumulate more than 1,450-fold the concentration of the investigated heavy elements in water rendering them of interest for use in phytoremediation studies of polluted waters. Given the absence of systematic water quality monitoring, heavy elements in plants, rather than sediments, provide a cost-effective means for assessing heavy element accumulation in aquatic systems during plant organ lifespan.