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Soil water repellency (hydrophobicity) prevents water from wetting or infiltrating soils, triggering changes in the ecosystems. This physical property is directly correlated to the erodibility grade of a soil. Wildfire events may develop, enhance, or destroy soil hydrophobicity, modifying the erodibility grade of a soil and increasing the loss of its most reactive layer (organic matter). To assess the main organic family of compounds (biomarkers) surrogates to fire-induced water repellency, a study was carried out on a fire-affected soil under eucalyptus canopy at two depths (0–2 and 2–5 cm) from Portugal. The potential soil water repellency was measured using the water drop penetration time (WDPT) test. The molecular characterization of hydrophobic biomarkers was carried out using analytical pyrolysis (Py-GC/MS) in combination with multivariate statistical analysis (PCA, MLR). The upper burned soil layer (0–2 cm) displayed a significant contribution of fresh biomass (lignin and polysaccharides), while the deepest (2–5 cm) one showed more humified organic matter (lipids). The soil hydrophobicity was directly correlated to non-polar organic compounds, such as lipids and polycyclic aromatic hydrocarbons (PAHs), and inversely to unspecific aromatic compounds. The combination of mass spectrometry techniques and chemometric analysis allowed obtaining a preliminary forecast model of hydrophobicity degree in fire-affected soil samples under eucalyptus canopy. This analytical approach opens the door to developing more sensitive mathematical models using molecular organic compounds to predict the alteration of hydrophobicity and other soil physical properties induced by fires. [ABSTRACT FROM AUTHOR]