This paper reports on the effects of human resettlement on the nutrient balance of the agroecosystems in Three Gorges Reservoir Area (TGRA) of China. The analysis used is the OECD (Organisation for Economic Co-operation and Development) 'Soil Surface Nitrogen Balance Model' and agricultural statistical data for the county level in 1985-2005. Spatial and temporal changes of nutrient balance and the impacts of resettlement on such changes were examined. The results demonstrate that rural resettlement has significantly increased soil surface nitrogen and phosphorous surplus since 2000. The structural transformation of agricultural activities from grain production to horticulture or forestry should be encouraged, and more people may need to be moved out of the TGRA to reduce nutrient water pollution.