The water quality in estuaries has been aggravated by the excessive nutrients from lands. Nitrogen compounds are one of the main factors for the coastal water eutrophication, especially the inorganic nitrogen in Changjiang River Estuary and Hangzhou Bay. Its concentration is much higher than the criterion of the Sea Water Quality Standard of the People's Republic of China (GB 3097-1997) so that it’s necessary to take the targeted measurements of the treatment and control as soon as possible. Nanzhu River located in Shanghai is taken as an example. It’s one of the main drainage channels along the Hangzhou Bay in the Taihu Lake Basin. Based on the evaluated pollution loads of the Total Nitrogen (TN) sources, the local rural sewage pollution is the maximum and after them the agricultural non-point pollution. To effectively improve the nearshore water quality, the TN load model has been established and calibrated to simulate the distribution character of TN in time and space coupling with the hydrodynamic sub-model, rainfall runoff sub-model and water quality sub-model by MIKE 11 software. The numerical results are shown that the max net inflows of TN come from the west tributaries in Nanqiao Town with about 56.06 t/a by 35% of the total net TN and 4.1x107 m3/year by 47% of the total net inflows. When a series of measures including reducing the non-point sources of the planting industry, upgrading and renovating the rural domestic sewage facilities, controlling the aquaculture and urban pollution are carried out simultaneously, the TN in Nanzhu River would be reduced to 1.94 mg/L, about 6% fall.