The LNAPL contamination affecting an industrial area of southeastern Sicily (Italy) is reported herein as a case study to analyze some peculiarities on its spatial evolution. The free-phase product of light hydrocarbons, leaked from a tank, deserved investigations due to its anomalous migration trend, which was not consistent with the static groundwater flow direction of the area. The collection of geological and hydrogeological data and their organization into a GIS database allowed reconstructing the evolutionary stage of the plume within the 2014–2020 time interval, providing some explanation to the scientific problem. The supernatant thickness was compared with the groundwater oscillation, leading to consideration on the aquifer typology. The causes of the peculiar migration trend were found in three main factors, among which the geological and geostructural ones gain a key relevance. Achieved results show that the rock mass fracturing and the presence of underground structures, probably of tectonic origin, are responsible in driving the contamination plume through a preferential path under the dynamic condition induced by anthropic activities. This supports the need of underground geological and geostructural knowledge when dealing with similar issues and when designing specific remediation measures; the case study presented herein demonstrates that the correct location of remedial measures is crucial for reclamation purposes. Furthermore, data were statistically analyzed looking for a relation between real and apparent supernatant thickness. Prediction equations, for a quick estimation of the contamination entity in such type of aquifers, are presented providing hints for future studies on other settings worldwide.