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A rapid and sensitive method is described for measuring perchlorate (ClO 4 − ), chlorate (ClO 3 − ), chlorite (ClO 2 − ), bromate (BrO 3 − ), and iodate (IO 3 − ) ions in natural and treated waters using non-suppressed ion chromatography with electrospray ionization and tandem mass spectrometry (NS-IC-MS/MS). Major benefits of the NS-IC-MS/MS method include a short analysis time (12 minutes), low limits of quantification for BrO 3 − (0.10 μg L −1 ), ClO 4 − (0.06 μg L −1 ), ClO 3 − (0.80 μg L −1 ), and ClO 2 − (0.40 μg L −1 ), and compatibility with conventional LC-MS/MS instrumentation. Chromatographic separations were generally performed under isocratic conditions with a Thermo Scientific Dionex AS16 column, using a mobile phase of 20% 1 M aqueous methylamine and 80% acetonitrile. The isocratic method can also be optimized for IO 3 − analysis by including a gradient from the isocratic mobile phase to 100% 1 M aqueous methylamine. Four common anions (Cl − , Br − , SO 4 2− , and HCO 3 − /CO 3 2− ), a natural organic matter isolate (Suwannee River NOM), and several real water samples were tested to examine influences of natural water constituents on oxyhalide detection. Only ClO 2 − quantification was significantly affected – by elevated chloride concentrations (>2 mM) and NOM. The method was successfully applied to quantify oxyhalides in natural waters, chlorinated tap water, and waters subjected to advanced oxidation by sunlight-driven photolysis of free available chlorine (sunlight/FAC). Sunlight/FAC treatment of NOM-free waters containing 200 μg L −1 Br − resulted in formation of up to 263 ± 35 μg L −1 and 764 ± 54 μg L −1 ClO 3 − , and up to 20.1 ± 1.0 μg L −1 and 33.8 ± 1.0 μg L −1 BrO 3 − (at pH 6 and 8, respectively). NOM strongly inhibited ClO 3 − and BrO 3 − formation, likely by scavenging reactive oxygen or halogen species. As prior work shows that the greatest benefits in applying the sunlight/FAC process for purposes of improving disinfection of chlorine-resistant microorganisms are realized in waters with lower DOC levels and higher pH, it may therefore be desirable to limit potential applications to waters containing moderate DOC concentrations ( e.g. , ∼1–2 mg C L −1 ), low Br − concentrations ( e.g. , <50 μg L −1 ), and circumneutral to moderately alkaline pH ( e.g. , pH 7–8) to strike a balance between maximizing microbial inactivation while minimizing formation of oxyhalides and other disinfection byproducts.