Hai Duong is a rapidly urbanizing province with a condensed network of rivers, located downstream of the Cau River Basin, one of the three most polluted river systems in Vietnam. Intensive agriculture and industrial development in the province has caused profound impact on the river water. This research aims to develop a material flow analysis (MFA) model, which can simulate and visualize nitrogen flows in Hai Duong province and its districts, to access the impact of agricultural activities and industrial parks on the surrounding environments. MFA was applied for Hai Duong province and its districts to estimate nitrogen flows in the whole province. The nitrogen loads to surface water, air, and soil/groundwater annually were 50,531 ± 10,801, 12,981 ± 1541, and 6055 ± 3121 tons, respectively. The quality of the developed model was assessed through a modified uncertainty analysis procedure. Also, MFA results of nitrogen loads to the water environment were consistent with the analytical results. Nitrogen was largely derived from agricultural activities and domestic and industrial wastewater. Environmental flows in the next 10 years and reasonable solutions for improving environmental quality in the province are proposed.