Chlorination is the most commonly used in disinfection to prevent from the bacterial growth in both intake and distribution pipelines or storage tanks. However, the disinfection treatment can result in an undesirable by-product, such a bromate (BrO3−), which is a suspected human carcinogen. Seawater has a high potential of BrO3− formation because of high bromide (Br−) concentration (around 65mg/L) which can be transformed by chlorination in disinfection process. Therefore, the measurement or monitoring of BrO3− formation is necessary. This study aims to apply the sensitive amperometric sensing system for detecting BrO3− in free chlorine condition. A linear dynamic ranged from 60 to 200nM of BrO3− even in 28μM free chlorine solution with a sensitivity of 108.8μA/μM. The detection limit level of BrO3− was 38.6nM and the limit of quantification value of BrO3− was 113.7nM (at pH7). This detection limit value was half of global guideline value for drinking water. The proposed technique had no noticeable interference to the sensing of BrO3− over various potentially interfering agents and other chlorinated disinfection by-products. The data measured by multilayered sensor system was in a good agreement for detecting BrO3− with validated data measured by using a conventional UV–vis spectroscopic method. As a final demonstration, the proposed amperometric sensing system would significantly contribute to the on-site detection of BrO3− concentration from chlorinating disinfection process within drinking water treatment plants, including desalination, and water quality monitoring applications.