There are a lot of factors to influence water environment evaluation. The mutual-effect is very complex. In order to reflect clearly the effects of different factors in water environment evaluation, the paper adopted fuzzy comprehensive evaluation method to deal with water environment. It is shown from study results that the fuzzy comprehensive method has good dependability for water environment evaluation. The method can calculate the main pollutants, provide data for reasonable water environment management and play reference role in other methods used in water environment evaluation.