This study investigates the influence of Polycyclic Aromatic Hydrocarbons (PAHs) driven contamination on microbial diversity and community structure in seawater and sediment samples from five sites in the Inner Saronikos Gulf and Elefsis Bay, Greece, two marine coastal areas under intense anthropogenic pressure. PAHs were quantified in both seawater (dissolved and particulate phase) and sediments. The molecular profiles of the determined PAH compounds indicate mixed petrogenic and pyrolytic sources, with low molecular weight (LMW) PAHs dominating seawater and high molecular weight (HMW) ones prevailing in sediments. High-throughput sequencing revealed distinct microbial communities, highlighting the use of microbial taxa as contamination bioindicators. Canonical Correspondence Analysis (CCA) grouped the bacterial communities according to PAH sources. The results describe pollutant-driven microbial responses and highlight the ecological risks of chronic PAH contamination in the study area.