A sensitive method is presented for the fast analysis of seven fuel oxygenates (methanol, ethanol, tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), tert-amyl methyl ether (TAME) and diisopropyl ether (DIPE)) and benzene, toluene, ethylbenzene and p-xylene (BTEX) in water samples. The applicability of a headspace (HS) autosampler in combination with a GC device equipped with a programmable temperature vaporizer (PTV) and a MS detector is explored. The proposed method achieves a clear improvement in sensitivity with respect to conventional headspace methods due to the use of the PTV. Two different packed liners with materials of different trapping strengths (glass wool and Tenax-TA) were compared. The benefits of using Tenax-TA instead of glass wool as packed material for the measurement of the 11 compounds emerged as better signal-to-noise ratios and hence better detection limits. The proposed method is extremely sensitive. The limits of detection are of the order of ng/L for six of the compounds studied and of the order of microg/L for the rest, with the exception of the most polar and volatile compound: methanol. Precision (measured as the relative standard deviation for a level with an S/N ratio close to 3) was equal to or lower than 15% in all cases. The method was applied to the determination of the analytes in natural matrixes (tap, river and sea water) and the results obtained can be considered highly satisfactory. The methodology has much lower detection limits than the concentration limits proposed in drinking water by the US Environmental Protection Agency (EPA) and the European Union for compounds under regulation.