Wastewater treatment plants have recently been identified as a significant pathway for the introduction of perfluoroalkyl surfactants (PASs) to natural waters. In this study, we measured concentrations and fate of several PASs in six wastewater treatment plants (WWTPs) in New York State. We also monitored and measured matrix effects (ionization suppression and enhancement) by postcolumn infusion and standard additions. Concentrations of perfluorooctanoate (PFOA) in effluents of the six WWTPs ranged from 58 to 1050 ng/L. Perfluorooctanesulfonate (PFOS) was also ubiquitous in effluents of these WWTPs, albeit at much lower concentrations (3-68 ng/L). Two of these WWTPs employed identical treatment processes, with similar hydraulic retentions, but differed only in that Plant B treated domestic and commercial waste, whereas Plant A had an additional industrial influence. We found that this industrial influence resulted in significantly greater mass flows of all of the PASs analyzed. Primary treatment was found to have no effect on the mass flows of PASs. Secondary treatment by activated sludge in Plant A significantly increased (p < 0.05) the mass flows of PFOS, PFOA, perfluorononanoate (PFNA), perfluorodecanoate (PFDA), and perfluoroundecanoate (PFUnDA). However, in Plant B, only the mass flow of PFOA was significantly increased. The observed increase in mass flow of several PASs may have resulted from biodegradation of precursor compounds such as fluorotelomer alcohols, which is supported by significant correlations in the mass flow of PFOA/PFNA and PFDA/PFUnDA. Furthermore, the masses of PFDA and PFUnDA were significantly correlated only after the secondary treatment. In Plant A, concentrations of odd-number PFCAs were greater than those of even-number PFCAs, and concentration decreased with increasing chain length (from C8 to C12). A different pattern was observed in sludge samples, in which the dominance of PFOA decreased, and PFDA and PFUnDA increased, suggesting preferential partitioning of longer-chain PFCAs to sludge.