The Agricultural Policy/Environmental eXtender (APEX) model is widely used for evaluating agricultural conservation efforts and their effects on soil and water. A key component of APEX application in Korea is simulating water quality impacts of rice paddies because rice agriculture claims the largest cropland area in the country. In this study, a computational module called APEX-Paddy is developed to simulate water quality with considering pertinent paddy management practices such as puddling, flood irrigation management. Data collected at two experimental paddy sites in Korea were used to calibrate and validate the model. Results indicate that APEX-Paddy performs well in predicting runoff discharge rate and nitrogen yield while the original APEX highly overestimates runoff rates and nitrogen yields on large storm events. With APEX-Paddy, simulated and observed flow and mineral nitrogen yield (QN) are found to be highly correlated after calibration (Nash & Sutcliffe Efficiency (NSE) = 0.87 and Percent Bias (PBIAS) = −14.6% for flow; NSE = 0.68 and PBIAS = 2.1% for QN). Consequently, the APEX-Paddy showed a greater accuracy in flow and QN prediction than the original APEX modeling practice using the SCS-CN method.