The aim of this study was to characterize samples of petroleum spills derived from the oily free-phase zone located in the subsurface of a petroleum refinery and to reveal the contained distinct petroleum fractions, thus enabling the identification of the spill origin. The samples were collected from different monitoring wells and were analyzed using gel permeation chromatography (GPC) combined with a UV-diode array detector. The PARAFAC algorithm was employed for the analysis of the 3-D experimental data matrix, which contained the areas under the chromatographic trace, measured for distinct time slices over the 270-440 nm UV range for the whole sample population. The application of the PARAFAC method revealed two significant elution profiles possessing characteristic UV signals, which were attributed to the gasoline and diesel fractions, respectively. A third elution profile was also identified which corresponded to biodegraded heavy fractions. The relative contribution of these compositional features to the oil spill samples was also identified. The presented method can be employed as a rapid and reliable fingerprinting tool in environmental studies, where petroleum pollutants of unknown composition are expected.