Perfluorinated compounds (PFCs) such as perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) have received worldwide attention because of their environmental persistence and widespread distribution. Because of the lack of robust analytical methods and standards to detect all of the PFCs, and their precursors and metabolic intermediates, a mass balance approach involving the determination of total fluorine (TF), followed by fractionation of samples to separately determine inorganic and organic fluorine, is needed. In this study, we have developed a method to determine low microg/L levels of total fluorine (TF) in seawater samples. Further, seawater samples were fractionated into organic and inorganic fractions by extraction with organic solvents, which were then analyzed for TF, extractable organic fluorine (EOF) and inorganic fluorine (IF; i.e., fluoride). Concentrations of known perfluorinated compounds (PFCs) including PFOS and PFOA were also determined in water samples by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to enable calculation of the fraction of fluorine that is contributed by PFCs to TF. A major proportion of fluorine in seawater was in the form of fluoride (>90% in locations not affected by direct discharges). Nevertheless, within the organofluorine fraction, a major percentage (60-90%) of fluorine still remains unknown in water samples, suggesting the occurrence of other fluorinated acids in addition to known perfluorinated acids. Further studies are needed to identify and quantify the unidentified organofluorines in seawater. Mass balance analysis of total organic fluorine (TOF) and EOF is important, if we are to understand transport and fate of fluorinated compounds in the environment, and if we are to identify the sources of unidentified fluorinated compounds.