Environmental pollution and its eco-toxicological impacts have become a large and interesting concern worldwide as a result of fast urbanization, population expansion, sewage discharge, and heavy industrial development. Nine heavy metals (Pb, Cd, Fe, Mn, Zn, Ni, Cu, Cr, and Co) were evaluated in 20 sediment samples from the estuaries of four major drains along the Mediterranean shoreline (Nile Delta coast) to determine the possible ecological effect of high heavy metal concentrations as well as roots and shoots of two common macrophytes (Cyperus alopecuroides and Persicaria salicifolia). For sediment, single- and multi-elemental standard indices were used to measure ecological risk. Data revealed high contents of heavy metals, for which the mean values of heavy metals in sediment followed a direction of Fe > Mn > Co > Zn > Cu > Ni > Cr > Pb > Cd, Fe > Mn > Co > Ni > Zn > Cu > Cr > Pb > Cd and Fe > Mn > Zn > Co > Cu > Ni > Cr > Pb > Cd for drains stream, estuaries, and Mediterranean coast, respectively. Mn, Cr, Zn, and Pb were found to be within Canadian Soil Quality Guidelines (CSQGD) and U.S. Environmental Protection Agency Guidelines (US-EPA) limitations, except for Zn and Pb in drain streams, which were above the US-EPA limits, whereas Cd, Co, Cu, and Ni indicated a high ecological risk index. This high quantity of contaminants might be linked to unabated manufacturing operations, which can bio-accumulate in food systems and create significant health issues in people. C. alopecuroides root demonstrated a more efficient accumulation of all metals than the shoot system. For most heavy metals, C. alopecuroides had the highest root BAF levels with the exception of Ni and Pb in P. salicifolia. As a result, C. alopecuroides might be employed as a possible phytoextractor of these dangerous metals, while P. salicifolia could be used as a hyper-accumulator of Ni and Pb. The policymaker must consider strict rules and restrictions against uncontrolled industrial operations, particularly in the Nile Delta near water streams.