The risk source identification focuses on the enterprise index such as industry category, the shortest distance from valley, away from the sensitive target process, and then constructs the risk source identification system. In the respect of weighting methods of index weight, the paper used new method witch is a combination improved analytic hierarchy process(AHP) and entropy value method to define the weight of each index and to build up weight evaluation method for risk source indicator. Using the fuzzy-based assessment method, the paper carried out comprehensive analysis and evaluation to typical watershed in northwest inland area and established the method of risk discern of water environment witch is fitted to the river basin. The method can provide strong technical support for water environment protection of the watershed.