No validated models in Europe are capable of simulating the environmental fate of pesticides under the specific conditions of rice fields. Rice water quality—vadose zone flow and transport (RICEWQ-VADOFT) is a model developed from the coupling of a surface runoff model (RICEWQ) and a vadose zone flow and transport model (VADOFT) for determining predicted environmental concentrations in paddy water and sediment, runoff, and groundwater. This study is intended to evaluate the capability of this model to simulate effectively the environmental fate of the herbicide pretilachlor in the paddy environment. A two-year field study conducted in a representative rice-cultivated area of northern Italy provided measured concentrations of pretilachlor in paddy water and sediment and also a limited number of observations on runoff losses. The model successfully predicted the water balance in the paddy field in both years. After limited calibration, the model predicted the fate of pretilachlor in paddy water and sediment with high accuracy. Agreement between predicted and measured concentrations of pretilachlor in both years was assessed statistically using several statistical indicators. For example, modeling efficiency (EF) values of 0.867 to 0.935 and 0.702 to 0.718 in paddy water and sediment, respectively, document the strong agreement between predicted and measured pesticide concentrations. The model predictions showed high agreement with the limited amount of measured runoff data in 2002. The model predicted that no significant amounts of pretilachlor would leach below the top 25 cm of the soil, although no measured data were available to evaluate the predicted results. A sensitivity analysis of the model to variables controlling pesticide partitioning to paddy sediment (VBIND, depth for direct partitioning of pesticide to bed sediment; VMIX, mixing velocity by molecular diffusion) revealed that the predictions of pesticide leaching were influenced strongly by those variables. Generally the RICEWQ-VADOFT model is a useful modeling tool for pesticide risk assessment in rice paddies.