Applying models to interpret soil, water and plant relationships under different conditions enable us to study different management scenarios and then to determine the optimum option. The aim of this study was using Water and Agrochemicals in the soil, crop and Vadose Environment (WAVE) model to predict water content, nitrogen balance and its components over a corn crop season under both conventional tillage (CT) and direct seeding into mulch (DSM). In this study a corn crop was cultivated at the Irstea experimental station in Montpellier, France under both CT and DSM. Model input data were weather data, nitrogen content in both the soil and mulch at the beginning of the season, the amounts and the dates of irrigation and nitrogen application. The results show an appropriate agreement between measured and model simulations (nRMSE < 10%). Using model outputs, nitrogen balance and its components were compared with measured data in both systems. The amount of N leaching in validation period were 10 and 8 kgha–1 in CT and DSM plots, respectively; therefore, these results showed better performance of DSM in comparison with CT. Simulated nitrogen leaching from CT and DSM can help us to assess groundwater pollution risk caused by these two systems.