Rapid socio-economic development in suburban areas of developing countries has induced changes in agricultural waste and nutrient management, resulting in water pollution. The study aimed at estimating agricultural nutrient cycles and their contribution to the water environment. A material flow model of nitrogen (N) and phosphorus (P) was developed focusing on agricultural activities from 1980 to 2010 in Trai hamlet, an agricultural watershed in Nhue-Day River basin, Vietnam. The model focused on the change in household management of human excreta and livestock excreta, and chemical fertilizer consumption. The results showed that the proportion of nutrients from compost/manure applied to paddy fields decreased from 85 to 41% for both N and P between 1980 and 2010. The nutrient inputs derived from chemical fertilizer decreased 6% between 1980 and 2000 for both N and P. Then, these nutrients increased 1.4 times for N and 1.2 times for P from 2000 to 2010. As of 2010, the total inputs to paddy fields have amounted to 435 kg-N/ha/year and 90 kg-P/ha/year. Of these nutrient inputs, 40% of N and 65% of P were derived from chemical fertilizer. Thirty per cent (30%) of total N input was discharged to the water bodies through agricultural runoff and 47% of total P input accumulated in soil.