In pesticide risk management in Japan, predicted environmental concentrations are estimated by a tiered approach, and the Ministry of the Environment also performs field surveys to confirm the maximum concentrations of pesticides with risk concerns. To contribute to more efficient and effective field surveys, we developed the Pesticide Chemicals High Resolution Estimation Method (PeCHREM) for estimating spatially and temporally variable emissions of various paddy herbicides from paddy fields to the environment. We used PeCHREM and the G-CIEMS multimedia environmental fate model to predict day-to-day environmental concentration changes of 25 herbicides throughout Japan. To validate the PeCHREM/G-CIEMS model, we also conducted a field survey, in which river waters were sampled at least once every two weeks at seven sites in six prefectures from April to July 2009. In 20 of 139 sampling site-herbicide combinations in which herbicides were detected in at least three samples, all observed concentrations differed from the corresponding prediction by less than one order of magnitude. We also compared peak concentrations and the dates on which the concentrations reached peak values (peak dates) between predictions and observations. The peak concentration differences between predictions and observations were less than one order of magnitude in 66% of the 166 sampling site-herbicide combinations in which herbicide was detected in river water. The observed and predicted peak dates differed by less than two weeks in 79% of these 166 combinations. These results confirm that the PeCHREM/G-CIEMS model can improve the efficiency and effectiveness of surveys by predicting the peak concentrations and peak dates of various herbicides.