Heavy metal contamination in both sediments and molluscs from the Egyptian Mediterranean coast was investigated. Seawater, sediments, and mollusc samples were collected from representative locations along the coastal area. Different representations of the data set, including, statistical methods (correlation matrix and cluster analyses), various sediment quality assessment methods, and bioaccumulation factor calculation, were combined to investigate the trends of heavy metals, identify pollution sources, and assess sediment quality from a toxicological point of view. The measurements of dissolved oxygen (DO) revealed to relatively well oxygenate surface water in all locations. There is a distinct change in the contents of heavy metals (Fe, Al, Zn, Cu, Ni, Cr, Pb, Cd, and Hg) among the sampling sediments. The statistical interpretations showed that the bio-availability of the studied heavy metals is controlled by different factors, including the geochemistry of sediments, the hydrology of the system, the uptake of metals from sediments, as well as human anthropogenic activities. Although, there are still certain points of the Egyptian Mediterranean coast with a relatively high concentration of toxic metals, the toxicological approach suggests that the risk for living organisms is not high, but, in the long run, toxicological implications can appear. These results can provide useful information for the local managers and decision makers.