A solid phase extraction-liquid chromatography tandem mass spectrometry (SPE-LC/MS/MS) analytical method for the analysis of perfluorinated compounds (PFCs) in water is presented. The method incorporates a stable isotope internal standard (IS) for each target analyte added prior to sample collection. Method validation for perfluorinated carboxylic acids (PFCAs) (C4–C12), perfluorinated sulfonic acids (PFSAs) (C4, C6, and C8), and perfluorooctane sulfonamide (PFOSA) in laboratory Milli Q water evaluated the following: (1) method accuracy and precision over the concentration range 0.025 ng mL−1 to 25 ng mL−1; (2) internal standard calibration; (3) quantitation of mixed branched and linear isomers of perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) with linear isomer calibration; (4) method minimum reporting levels (MRLs) (Shoemaker et al, http://www.epa.gov/nerlcwww/Method%20537_FINAL_rev1.1.pdf, and Winslow et al, Environ. Sci. Technol., 2006, 40, 281–288); and (5) 28 day holding time at the MRL, low, and mid range of the calibration range. IS calibration with IS addition to the sample bottle prior to sample collection demonstrated an overall method accuracy of at least 100 ± 10% with a precision of ±15% and a 28-day sample holding time at the MRLs for all target analytes. Method application to groundwater, production facility non-contact cooling water, and production facility wastewater treatment effluent samples demonstrated a method accuracy of at least 100 ± 19% with a precision of ±25% for all target analytes.