The SPEC model (Predicted Environmental Concentrations in agricultural Soils) was developed and improved for the simulation of pesticide runoff. The model was applied to the Sakaecho upland bare soil field (Tokyo, Japan) to predict runoff water, sediment concentration in runoff water, pesticide concentrations in runoff water, and runoff sediment (clothianidin and imidacloprid) under artificial rainfall conditions. The results showed that the simulated time to first runoff agreed very well with the observed data. The simulated cumulative runoff, sediment yield, and imidacloprid concentration in sediment agreed well with the observed data (Nash–Sutcliffe Efficiency (NSE)>0.75). The simulated runoff rate agreed reasonably well with the observed data (NSE >0.5). The predicted clothianidin concentrations in sediment and in runoff water had acceptable agreement with the observed data (NSE >0). The results implied the model’s potential to predict runoff water, sediment yield, and pesticide runoff.