Gas-chromatography (GC) analysis of carboxylic acids is limited by the high polarity and low volatility of most of these compounds. Boron trifluoride (BF₃) mediated alkylation reactions is one of the most commonly used derivatization methods for making carboxylic acids GC compatible. A semi-automated BF₃·EtOH (ethanol) derivatization method was optimized for comprehensive two-dimensional gas chromatography high-resolution mass spectrometry (GC × GC–HR MS) analysis of carboxylic acids in solid phase extraction (SPE) extracts of oil polluted water. The optimal derivatization method were found to be with addition of 300 μL BF₃·EtOH per 200 μL sample and reaction at 75 °C for 24 h. Derivatives of eight selected acids (aliphatic, mono- and di-aromatic) were stable over 12 h with relative standard deviations (RSDs) of 2.0–10.7 %, the derivatization method was repeatable (RSDs of 3.2–17.2 %), detection limits (DL) and limit of detections (LODs) was in the range of DL = 0.53–1.63 ppb and LOD = 0.19–2.51 ppb for pure acid standards, and DL = 0.18–3.41 ppb and LOD = 0.28–5.46 ppb for matrix matched acid standards. Finally, the method was validated on the acidic fraction of a mixed anion-exchange SPE of oil polluted water. Thousands of degradation products from parent alkylated polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons, such as aliphatic acids and mono-, di- and tri- aromatic acids were analyzed by the applied method and compound groups were tentatively identified.