Through monitoring the current situation of water quality in Manas River, the paper analyzed the main pollutants such as ammonia, fluoride and chloride in Manas River. According to the categories and objectives of water quality of water function zoning,it used fuzzy comprehensive evaluation to estimate the assimilative capacity of Manas River. The countermeasures of further improving assimilative capacity can reduce the pollution factors witch exceed the maximum dirt holding capacity so that the concentration of pollutants achieve at emission standards and then discharge.