To evaluate nutrient dynamics with different fertilization in paddy field and develop water quality model, mass balance analysis was performed during growing season of 2001-2002 in field experimental plots irrigated with groundwater. As a result of water balance analysis, most of outflow was surface drainage as about half of total outflow and about 500mm was lost by evapotranspiration. The water budget was well balanced. The runoff from paddy field was influenced by rainfall and forced drain. Especially runoff during early cultural periods more depends on the forced drain. As a result of mass balance analysis, most of nutrient was input by fertilization and lost by plant uptake. Significant amount of nitrogen were supplied by precipitation and input from upper paddy field, comprising 12%∼28% of total inflow. Nutrient loading by surface drainage was occurred showing about 15%∼29% for T-N and 6%∼13% for T-P. The response of rice yield with different fertilization was not significant in this study. Water quality model for paddy field developed using Dirac delta function and continuous source was calibrated and validated to surface water quality monitoring data. It demonstrates good agreement between observed and simulated. The nutrient concentration of surface water at paddy field was significantly influenced by fertilization. During early cultural periods when significant amount of fertilizer was applied, surface drainage from paddy field can cause serious water quality problem. Therefore, reducing surface drainage during fertilization period can reduce nutrient loading from paddy fields. Shallow irrigation, raising the weir height in diked rice fields, and minimizing forced surface drainage are suggested to reduce surface drainage outflow.