Freshwater is an essential resource which should be wisely used and shared between the different sectors especially in rapidly developing countries such as Vietnam. In Vietnam, agricultural production and farming systems have been intensified and diversified to follow the growing economy and food demands. However, intensification of agriculture resulted in environmental damage such as eutrophication of surface and ground water, and soil degradation. Sustainable management of soil and water is thus needed to share limited resources between farming systems such as rice, vegetables and animal husbandry. However, the diversified structure of the farming systems makes it difficult to evaluate the impacts from the integrated farming systems. To cope with the diversity and complexity, a mathematical model-based approach would be useful in describing these complex processes and their interactions. The present study aims to develop a mathematical model to simulate the dissolved nitrogen dynamics in a paddy field in the Red River Delta Vietnam. A series of field experiments under different fertilization conditions was carried out in an experimental paddy field of Hanoi University of Agriculture, Vietnam. Ammonium and nitrate nitrogen were monitored in the paddy field water and adjacent canal water, based on which a mathematical model was developed to estimate the concentration of dissolved nitrogen in surface water of the paddy field. As a result, the present model could represent the dynamics of the dissolved nitrogen in relation to farming practices such as fertilizer application. Despite the applicability, further improvement of the model considering nitrogen budget on the soil-water interface would be necessary in order to better represent the nitrogen dynamics and optimize fertilizer applications in both timing and amount.