In order to monitor pollutants from urban areas to coral reefs, metal contents in Porites coral samples collected from the Hija River mouth and at nearby sites from the estuary were analyzed. The corals were cleaned by oxidative and reductive treatments to effectively eliminate detritus and organic materials. Metal-to-calcium (Me/Ca) ratios in the samples were determined by ICP-MS. Filtered samples of river water were also measured similarly for metal concentrations. The extent of anthropogenic contribution by riverine input was assessed by comparing the Me/Ca values in corals to those of Rukan-sho, an unpolluted coral reef. High riverine inputs of Mn, Cd, Zn and Ag were observed from Me/Ca values in the coral samples. Manganese in the coral samples showed strong dependence on salinity, varying inversely to the distance from terrestrial sources. Considering a lead background of 25.0 nmol/mol measured in the Rukan-sho corals, Pb/Ca in corals of the Hija River estuary that are two and three times higher may indicate lead enrichment in the river mouth. Because Pb is only moderately high in the Hija River water compared to its concentration in surface seawater, lead may have accumulated in the estuarine water and sediments, resulting in an elevated concentration of lead available for coral uptake.