In view of the water impact of environmental risk of industrial enterprises in the Three Gorges Reservoir, based on the existing methods of water environmental risk assessment and integrated the Germany detailed list assessment method; we have established a brand-new index system which could meet with the Three Gorges Reservoir water environment risk evaluation, and the system has the feature of quantitative indicators and risk classification. Site Case analysis showed that: evaluation results and the qualitative judgment are on the spot consistent with the environment Supervisory department, which demonstrated that the risk assessment system is reasonable and has easier operability. Meanwhile the system could help the enterprise and the environment Supervisory department to investigate water environment hidden danger, reduce the enterprise water environment risk effectively and provide the scientific basis for the environment Supervisory management's decision-making and the management.