A direct, robust, accurate and highly sensitive method for oxyhalide species in natural waters, including seawater, using suppressed ion chromatography coupled with mass spectrometry (IC-MS) is described. The method utilised a high capacity, high efficiency anion-exchange column (Dionex IonPac AS11-HC, 4 mm, 2 × 250 mm), with the separation achieved using an electrolytically generated potassium hydroxide gradient, delivered at 0.380 mL min⁻¹. Applying the method, detection limits for iodate, bromate, and chlorate in seawater after direct sample injection (20 μL injection volume, samples diluted 10-fold), were 11, 30 and 13 ng L⁻¹ (ppt), respectively. Standard addition calibrations to ozonated seawater samples were linear, in all cases R² > 0.999 (n = 10), with intra-day repeatability of 3.7, 11.2 and 1.8 % RSD (n = 10) for a low-level standard mixture (0.30 μg L⁻¹ of iodate, 0.15 μg L⁻¹ of bromate, and 1.50 μg L⁻¹ of chlorate). The method was applied to the analysis of seawater samples taken pre- and post-disinfection points within a recirculating aquacultural system. Iodate, bromate and chlorate were detected as the main oxyanionic disinfection by-products, demonstrating the practical utility of the new method as a valuable tool for monitoring changes to seawater composition following disinfection treatments.