A rapid and sensitive method is described for measuring perchlorate (ClO₄⁻), chlorate (ClO₃⁻), chlorite (ClO₂⁻), bromate (BrO₃⁻), and iodate (IO₃⁻) 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 BrO₃⁻ (0.10 μg L⁻¹), ClO₄⁻ (0.06 μg L⁻¹), ClO₃⁻ (0.80 μg L⁻¹), and ClO₂⁻ (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 IO₃⁻ analysis by including a gradient from the isocratic mobile phase to 100% 1 M aqueous methylamine. Four common anions (Cl⁻, Br⁻, SO₄²⁻, and HCO₃⁻/CO₃²⁻), 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 ClO₂⁻ 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 ClO₃⁻, and up to 20.1 ± 1.0 μg L⁻¹ and 33.8 ± 1.0 μg L⁻¹ BrO₃⁻ (at pH 6 and 8, respectively). NOM strongly inhibited ClO₃⁻ and BrO₃⁻ 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.