Recent increase in global consumption of rice led to increased demand for sustainable water management in paddy cultivation. In this study, we propose an enhanced paddy simulation module in the SWAT model to evaluate sustainability of paddy cultivation. Enhancements added to SWAT are: 1) to modify water balance calculation for impounded fields, 2) to add an irrigation management option for paddy fields, which is characterized by flood irrigation with target water depth, and 3) to add puddling operation that influences water quality and infiltration rate of top soil layer. In a case study, the enhanced model, entitled SWAT-Paddy, was applied to an agricultural watershed in Japan. Results showed that the SWAT-Paddy successfully represents paddy cultivation, water management, and discharge processes. Simulated daily discharge rates with SWAT-PADDY (R2=0.8) were superior to SWAT2012 result (R2=0.002). SWAT-Paddy allows simulating paddy management processes realistically and thus, can enhance model accuracy in paddy-dominant agricultural watersheds.