Aquatic ecosystems act directly or indirectly as sinks for heavy metals, which persists for longer times in the biogeochemical cycle and poses high ecological risks and thus, it represents a major worldwide concern. To evaluate the metal contamination in the Nile Delta, twenty sites along both Rosetta and Damietta branches were investigated. Most heavy metals concentrations are above the sediments quality guidelines. The Contamination Factor (CF), Pollution Load index (PLI), and geo-accumulation index (I geo) indicated that the sediments are moderately to extremely polluted by Ni, Cd, Cr, Cu, Pb, and Zn. A trend of increasing metals concentration towards the Mediterranean was observed and attributed to historical sinking of heavy metals in the sediment, where many agricultural drains bringing mixed wastewater. Cluster analyses support the latter and indicated that the heavy metals, which clustered together, may have the same source (i.e. anthropogenic). Non-metric Multidimensional Scaling, Analysis of Similarity (ANOSIM), and Partial Least Square (PLS) regression confirmed that the distance along the river is the major predictor of the observed metal concentrations, while sediment grain–size has no or very minor effect. The lower hydrodynamics associated with the construction of Aswan High-Dam in 1964 and the developed agricultural system in addition to arid climate with scarce rainfall, all leave no chance for natural annual flooding. Therefore, freshening up of the sediments was prohibited. The marinating of well-controlled flooding may erode the upper contaminated portion of river sediments, dilute the metal concentrations, and improve the sediments quality.

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