AbstractLiquid chromatography/mass spectrometry (LC/MS)‐based methods were developed for the analysis of 10 resin acids and five fatty acids in process waters of paper industries. No fragmentation of target compounds was observed using atmospheric pressure chemical ionization (APCI) with negative ionization. The [M − H]− ion permitted the individual quantification of fatty and aromatic resin acids, whereas the non‐aromatic resin acids presented a single and common ion at m/z 301. Separation with two columns of different polarity permitted peak confirmation. The method that used a C8 column with 2‐propanol in the mobile phase allowed a certain separation and identification of the non‐aromatic resin acids, whereas the method using a C18 column provided detection limits 10‐fold lower for fatty acids. Limits of detection were 0.10 ng for all compounds. Direct sample introduction was compared with liquid–liquid extraction, with similar recoveries (70–101%). Whereas slightly lower detection limits were obtained with liquid–liquid extraction, better reproducibility was observed for direct sample introduction. Resin and fatty acids were determined in process waters of several paper industries. Palmitic, dehydroabietic and non‐aromatic resin acids were encountered in most water samples, at levels between 22 and 403 µg l−1. LC/MS with direct sample introduction was found to be a good alternative to traditional liquid–liquid extraction and gas chromatography for the analysis of such compounds since no derivatization was required and sample manipulation was minimal. Copyright © 2003 John Wiley & Sons, Ltd.