In the subsurface drainage system, there is a high potential for nitrate leaching, causing the pollution of both surface and ground water. In this research, a simple but comprehensive process-based model was developed for simulating the water flow and nitrogen dynamics. Processes considered in this model included all the important processes involved in nitrogen transformations, as well as nitrogen traort. Nitrogen transformation processes comprised fertilizer dissolution, nitrification, denitrification, ammonium volatilization, mineralization and immobilization. The nitrogen traort processes included nitrogen uptake by the plant, soil adsorption, upward flux, surface runoff losses and drain losses in the fields with the drainage network. For model evaluation, the measured data obtained from Imam agro-industrial Company, in Khuzestan, Iran, were used. Computed RMSE of the simulated water table, the drainage discharge rate, nitrate and ammonium concentration in drainage water were determined to be 14.58cm,1.82mm/day,1.73mg/L and 0.48mg/L, respectively. The results indicated a good agreement between the observed and simulated data. This model could be, therefore, used for fertilizer management, thereby reducing the concentration of nitrate and ammonium in the drainage water and helping to prevent the environmental pollution. Key words: Nitrogen simulation model, subsurface drainage system, System dynamics approach, Drainage water quality modeling.