Goiter is an important health problem all over the world and iodine deficiency is its most common cause. Perchlorate, thiocyanate and nitrate (called as major NIS inhibitors) are known to competitively inhibit iodide uptake by the thyroid gland and thus, human exposure to major NIS inhibitors is a public health concern. In this study, an ion chromatographic method for the determination of most common NIS inhibitor ions in drinking waters was developed and validated. This is the first study where an analytical method is used for the determination of major NIS inhibitors in drinking water by an ion chromatography system in a single run. Chromatographic separations were achieved with an anion-exchange column and separated ions were identified by a conductivity detector. The method was found to be selective, linear, precise accurate and true for all of interested ions. The limits of the detections (LOD) were estimated at 0.003, 0.004 and 0.025 mg L−1 for perchlorate, thiocyanate and nitrate, respectively. Possible interference ions in drinking waters were examined for the best separation of NIS inhibitors. The excellent method validation data and proficiency test result (Z-score for nitrate: −0.1) of the FAPAS® suggested that the developed method could be applied for determination of NIS inhibitor residues in drinking waters. To evaluate the usefulness of the method, 75 drinking water samples from Antalya/Turkey were analyzed for NIS inhibitors. Perchlorate concentrations in the samples ranged from not detected (less than LOD) to 0.07 ± 0.02 mg L−1 and the range of nitrate concentrations were found to be 3.60 ± 0.01 mg L−1 and 47.42 ± 0.40 mg L−1. No thiocyanate residues were detected in tested drinking water samples.