Cross correlation of coastal ecosystem alteration among three areas was investigated; two of them located along the Egyptian Mediterranean coast and the third one along the Gulf of Suez. Sediment textures, phosphorus forms, organic carbon, total carbonate content, water content, and pH were analyzed for collected short-core samples to reveal the variations and the relevant factors influencing the coastal depositional environments at the three sites. Geographic locations and relevant conditions combined with the anthropogenic stressors, corresponding to associated sources and magnitude of pollution, are considered as major affected elements in bottom habitats. The regional comparison between the two sites located along the Mediterranean Sea indicates a distinct gradient in the ecosystem and controlling factors from the west to the east. Alexandria site is represented as a typical near-shore oligotrophic, well-ventilated and unpolluted environment, attributed to an increase in water activity revealing a high-energy erosive environment. While, the site of Port Said is reflected as a highly stressed coastal environment, influenced by freshwater flush discharged from the nearby local outlet, developing strong and continuous wash out of seabed sediment. The Suez site is induced by tense industrial and domestic pollution, corresponding to the propagation of the anthropogenic impact, coupled with the significant effect of a hypersaline environment.