The study area is the Thriassion Plain, an important area, in antiquity, surrounding the famous ancient town of Eleusis, 20 km west of Athens. The modern town and port and the entire area were heavily industrialized (1965–1995) coupled with unregulated urban and agricultural development. The presence of two crude oil refineries and other oil-related industries have strongly impacted the entire environment, including soils, waters and sediments of the broader area. The purpose of this work is to better understand how a multi-layered groundwater system affects the potential underground spread of certain fuel volatile compounds, namely the BTEX (benzene, toluene, ethylbenzene and total xylenes) as well as their attenuation after their direct or indirect release into the aquifer system. The spatial distribution of BTEX in groundwaters show that they were concentrated mainly in four rather restricted locations. Three of them were spotted, as expected, in the close vicinity of known pollution sources (a military airfield and two crude oil refineries). The other one corresponds to an abandoned site with no outstanding pollution sources where wells exist, eventually used for illegal dumping of oily wastes. It is important that the concentrations decrease significantly from autumn to spring. This decline could be characterized as natural attenuation, related to natural dilution phenomena and a flushing out of pollutants discharging through underwater springs to the sea during the rainy period (October to April). This, in turn, could be associated to the specific geological conditions affecting the hydrology, such as the unconsolidated non-permeable deposits and the multi layered formations of the area’s aquifers.