We developed the method for estimating the region-specific predicted paddy pesticide concentrations in river in Tier 2 level (PEC_Tier2) for 29 pesticides. The important region-specific parameters of environmental conditions, which are river flow, paddy rice cropped area, and pesticide usage ratio, were prepared at 350 river flow monitoring sites in Japan. Estimated region-specific PEC_Tier2 suggested that the property of horizontal distribution, effect of each parameter for PEC calculation, and relative position of PEC_Tier2 calculated by standard scenario differed among pesticides. The calculation of region-specific PEC_Tier2 was validated by comparing with measured concentrations in Sakura river (Ibaraki prefecture). Differences between measured and predicted concentrations were within 10-folds for all but one pesticide. This suggests that preparing region-specific parameters (river flow, paddy rice cropped area, and pesticide usage ratio) enable to largely predict realistic environmental concentration for various kind of pesticide use.