A trace analytical method was developed for the determination of seventeen specific perfluorinated chemicals (PFCs) in environmental and drinking waters. The objectives were to optimize an isotope-dilution method to increase the precision and accuracy of the analysis of the PFCs and to eliminate the need for matrix-matched standards. A 250 mL sample of environmental or drinking water was buffered to a pH of 4, spiked with labeled surrogate standards, extracted through solid phase extraction cartridges, and eluted with ammonium hydroxide in methyl tert-butyl ether: methanol solution. The sample eluents were concentrated to volume and analyzed by liquid chromatography/tandem mass spectrometry (LC-MS/MS). The lowest concentration minimal reporting levels (LCMRLs) for the seventeen PFCs were calculated and ranged from 0.034 to 0.600 ng/L for surface water and from 0.033 to 0.640 ng/L for drinking water. The relative standard deviations (RSDs) for all compounds were <20% for all concentrations above the LCMRL. The method proved effective and cost efficient and addressed the problems with the recovery of perfluorobutanoic acid (PFBA) and other short chain PFCs. Various surface water and drinking water samples were used during method development to optimize this method. The method was used to evaluate samples from the Mississippi River at New Orleans and drinking water samples from a private residence in that same city. The method was also used to determine PFC contamination in well water samples from a fire training area where perfluorinated foams were used in training to extinguish fires.