The use of drainage water in the irrigation of agroecosystem is associated with environmental hazards, and can pose threats to human health. Nine heavy metals (Fe, Mn, Zn, Cu, Co, Cr, Ni, Cd and Pb) along three main drains in the middle Nile Delta were measures in the sediments, roots and shoots of three common macrophytes (Echinochloa stagnina, Phragmites australis and Typha domingensis). The physicochemical characteristics, as well as the enrichment factor (Ef), contamination factor (Cf), geoaccumulation index (Igeo), ecological risk factor (Er), degree of contamination (Dc) and potential ecological risk index (PERI), were determined for sediment. The metal bioaccumulation factor (BAF) and translocation factor (TF) were assessed for plants. Data revealed high contents of Cr, Zn and Cd in the upstream of the drains, while Mn, Cu and Ni were recorded in high concentrations in the downstream. Mn, Cr, Co, Cu, Ni and Zn were recorded to be within EU (2002), CSQGD (2007) and US EPA (1999) limits, while Cd and Pb showed high a ecological risk index. This high concentration of pollutants could be attributed to unremitting industrial activities, which can bioaccumulate in the food chains and cause serious problems for humans. The root of P. australis showed the effective accumulation of most of the elements, while T. domingensis revealed the highest accumulation of Pb. However, the highest BAF shoot value was found in T. domingensis for most of the heavy metals, except for Fe and Zn in P. australis and Mn in E. stagnina. Thus, P. australis could be used as a potential phytoextractor of these hazardous metals, as an eco-friendly and cost-efficient method for remediation of the polluted drains. Further, T. domingensis could be integrated as a hyperaccumulator of Pb. Strict laws and regulations must be taken into consideration by the policymaker against unmanaged industrial activities, particularly near the water streams in the Nile Delta.