Understanding tropical nutrient dynamics is essential for quantifying marine productivity. In tropical and subtropical oceans, however, the spatial and continuous observation of nutrients has been scarce because of low nutrient concentration. The nitrogen isotopes of organic nitrogen in coral skeletons (δ15Ncoral) could be used to record nitrogenous nutrient origins at oceanic surfaces. Here, we show the intra- and inter-reef variations of δ15Ncoral in the western Pacific. The zonal distribution of δ15Ncoral was found inside a coral reef corresponding with δ15N of seawater nitrate (δ15Nnitrate). The extended analysis of δ15Ncoral among various coral reefs also shows a latitudinal gradient from tropical to temperate in the western Pacific. The δ15Ncoral records high-resolution dynamics of nitrogenous nutrients through the geologic time scale.