Nutrient concentrations at the nanomolar level were monitored in the East China Sea and the Philippine Sea during summer using a continuous underway system with a highly sensitive colorimetric method. Concentrations of both nitrate and soluble reactive phosphorus (SRP) varied generally at <10 nM. However, nitrate frequently showed local elevations of 20 to >1000 nM at a horizontal scale of <10 km to tens of kilometers compared with neighboring waters. These nitrate patches were grouped into three types according to the associated environmental conditions with (1) lowered salinity and no changes in SRP and in vivo chlorophyll fluorescence, (2) lowered temperature and elevations of SRP and in vivo chlorophyll fluorescence, and (3) no consistent environmental variations. The first type was ascribed to rainfall, which is rich in nitrate but phosphate free. The second type was formed near islands/landmasses and was ascribed to upwelling or intense vertical mixing. The third type was not characterized and was considered to include several sources. Nine out of 20 nitrate patches belonged to the first type. Within each of these nine patches, nitrate concentration was negatively correlated with salinity. By extrapolating this correlation, nitrate concentrations in the rainwater were estimated to be within 0.14-6.2 M, which is well within the reported concentrations of nitrate in rainwater. On the basis of the estimated nitrate concentrations and amount of precipitation, nitrogen supply from rainfall in the study area was evaluated to be in the same order as that of diffusive upward flux and N2 fixation in summer.