In this review, we provide information on the occurrence and major sources of organic pollutants in the Aegean Sea and especially polycyclic aromatic hydrocarbons (PAH) and organochlorinated compounds (PCBs and DDTs) which are the most well-studied polluting substances in the area. Some information is also given on pharmaceuticals and other polar compounds belonging to the general category of emerging pollutants. Regarding PAH, some hotspots of pyrolytic compounds were identified, which are closely related to coastal anthropogenic activities, but pollution is usually restricted in small marine areas around their sources. In offshore areas, the concentrations of the considered PAH compounds were generally low, comparable to those reported in relatively nonpolluted Mediterranean marine sites. Their molecular profile and diagnostic indices reveal mixed contributions from both pyrolytic and petrogenic sources. Organochlorinated compounds were generally detected in very low concentrations in all studied areas, whereas some pharmaceuticals were measured in coastal areas that are directly influenced from wastewater treatment plants’ effluents.