The development of modeling technology to adequately simulate water and pesticide movement within the rice paddy environment faces several challenges. These include: (1) adequately representing ponded conditions; (2) the collection/implementation of temporal/spatial pesticide application data at field scales; (3) the integration of various mixed-landuses simulation schemes. Currently available models do not fully consider these challenges and results may not be sufficiently accurate to represent fate and transport of rice pesticides at watershed scales. Therefore, in this study, an integrated simulation system, "RiceWQ-AnnAGNPS", was developed to fully address these challenges and is illustrated in a California watershed with rice farming practices. The integrated system successfully extends field level simulations to watershed scales while considering the impact of mixed landuses on downstream loadings. Moreover, the system maintains the application information at fine spatial scales and handles varying treated paddy areas via the "split and adjust" approach. The new system was evaluated by investigating the fate and transport of thiobencarb residues in the Colusa Basin, California as a case study. Thiobencarb concentrations in both water and sediment phases were accurately captured by the calibrated RiceWQ model at the edge of field. After spatial upscaling, the integrated system successfully reflected both the seasonal pattern of surface runoff and the timing of monthly thiobencarb loadings. Incorporating future enhancements can further improve model performance by including more detailed water drainage schedules and management practices, improving the accuracy of summer runoff estimations, and incorporating a more sophisticated in-stream process module. This integrated system provides a framework for evaluating rice pesticide impacts as part of a basin level management approach to improve water quality, which can be extended to other rice agrochemicals, or other areas with fine-scale spatial information of pesticide applications.