As industry and population increase rapidly, the pollution of water environment has become a main factor influencing the sustainability of economic development in Taihu Basin. In order to achieve the integrated development in economy and environment protection, the implementation of total quantity control of pollutant discharge is important. In the study areas of Meiliang Bay and Zhushan Bay, we made a comprehensive research on situations of area economy, industrial structure, landuse and status of pollutant sources. Nested grid hydrology model and water quality model have been established to calculate regional water environmental capacity and pollutant reduction. Based on the water function and water areas, the water environmental capacity was assigned to every town (settlement). Thus the aim of total quantity control in different periods of each town and the plan of control and reduction of main pollutants have been established. The solution of pollutant control of each source in different periods has been proposed. Qualifying rate of regional water quality in river network areas will reach 80% by the year of 2015 after the plan implemented. The plan will provide technical support for the water environmental management of Taihu Basin.