The effects of water and pesticide management practices on ponded water pesticide concentrations in a paddy plot were analysed using the RICEWQ model. The molinate which is a herbicide widely used in rice culture, and frequently detected in paddy environment was selected. In a previous study, the RICEWQ model was successfully calibrated with field data obtained from a paddy plot in Daegu. The calibrated model was run using water and pesticide management scenarios with a set of measured meteorological data for 1997-2006 in Daegu. For all three ponded water depths with the label rate application, the amount of molinate dissipated in ponded water and volatilized accounted for more than 70%, and the runoff losses were less than 9%. The molinate losses through drainage in the very shallow ponded depth showed 40% less than that in deep ponded depth. Comparing with the deep and shallow ponded depth, the very shallow depth was the best with regards to the reduction of molinate runoff losses. Simulations with different pesticide application rates, label rate and double label rate, showed molinate concentrations in the ponded water increased linearly with the application rate increase.