Environmental dredging is an efficient means to counteract the eutrophication of water bodies caused by endogenous release of nitrogen and/or phosphorus from polluted sediments. The huge operational cost and subsequent disposal cost of the dredged polluted sediments, as well as the adverse effect on the benthic environment caused by excessive dredging, make the currently adopted dredging methods unfavorable. Precise dredging, i.e., determining the dredging depth based on the pollution level, not only significantly decreases the costs but also leaves a uniform favorable environment for benthos. However, there is still no feasible process to make this promising method executable. Taking a river heavily polluted by organic compounds as an example, we proposed an executable precise dredging process, including sediment survey, model establishment, data interpolation, and calculation of dredging amount. Compared with the traditional dredging method, the precise one would save 16 to 45% of cost according to different pollutant removal demands. This precise dredging method was adopted by the National Water Project of China to treat the endogenous pollution of Nanfei River in 2010. This research provides a universal scientific and engineering basis for sediment dredging projects.