Two quantitative methods using high-performance liquid chromatography (HPLC) combined with triple quadrupole tandem mass spectrometry (MS/MS) were developed to determine perfluoroalkyl and polyfluoroalkyl substances (PFASs) in aqueous samples. The first HPLC-MS/MS method was applied to 47 PFASs of 12 different substance classes with acidic characteristics such as perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkane sulfonic acids (PFSAs), as well as precursor substances and biotransformation intermediates (e.g., unsaturated fluorotelomer carboxylic acids). In addition, 25 (13)C-, (18)O-, and (2)H-labeled PFASs were used as internal standards in this method. The second HPLC-MS/MS method was applied to fluorotelomer alcohols (FTOHs) and perfluorooctane sulfonamidoethanols as these compounds have physicochemical properties different from those of the previous ones. Accuracy between 82% and 110% and a standard deviation in the range from 2% to 22% depending on the substances were determined during the evaluation of repeatability and precision. The method quantification limit after solid-phase extraction ranged from 0.3 to 199 ng/L depending on the analyte and matrix. The HPLC-MS/MS methods developed were suitable for the determination of PFASs in aqueous samples (e.g., wastewater treatment plant effluents or influents after solid-phase extraction). These methods will be helpful in monitoring campaigns to evaluate the relevance of precursor substances as indirect sources of perfluorinated substances in the environment. In one exemplary application in an industrial wastewater treatment plant, FTOHs were found to be the major substance class in the influent; in particular, 6:2-FTOH was the predominant compound in the industrial samples and accounted for 74% of the total PFAS concentration. The increase in the concentration of the transformation products of FTOHs in the corresponding effluent, such as fluorotelomer carboxylic acids, unsaturated fluorotelomer carboxylic acids, n:3 polyfluorinated saturated carboxylic acids (n indicates the number of nonfluorinated carbon atoms), and PFCAs, indicated biotransformation of FTOHs or their derivatives during wastewater treatment. However, only 33 mol% of the total amount of PFASs present in the influent was quantified in the corresponding effluent. Graphical abstract Method development of an HPLC-MS/MS multi-method for the determination of PFASs in aqueos samples.