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In order to know the environmental capacity, prevent the continual deterioration of the water quality of Fen River, and promote the harmonious development of economy and aquatic environment, the formula for calculating water environmental capacity of each reach was derived from generalizing the outfall based on the 1-D steady state water quality model. In accordance with the existing specials of water quality and hydrology data and the discharge distribution of the Fen River, the COD and NH3-N were selected as the main control factors of pollution which are the largest share of pollutants. The capacity of COD and NH3-N were studied for the average flow of the river at driest month under a different guaranteed rate from 1994 to 2006. The studies of this paper provide a scientific basis for resources protection and management of Fen River.