A new spectrophotometric method based on a liquid waveguide capillary cell for an enhanced detection was developed to measure nanomolar iodate concentrations. This method has a detection limit and precision of 1– 2 nmol/L, which is equivalent to 10％ that of conventional methods, a recovery of 97.7％–104.0％, and a working range of 10–120 nmol/L. Water samples were collected from three estuaries and one coastal ocean for testing, and the proposed technique detected as low as 11 nmol/L and 18 nmol/L iodate in these samples. This newly developed method is helpful in understanding the biogeochemical cycle of iodine in nature.