It has been a more complex problem for water quality assessment. And its aim is to well and truly evaluate its degree of pollution for bodies of water, which will be easy to provide some principled projects and criterions for water resource’s protection and their integration application. So, a water quality assessment method based on Multiclass Fuzzy Support Vector Machine is put forward. and a two-step cross-validation was used to search for the best combination of parameters to obtain an optimal training model. The test results show that the method proposed in this paper has an excellent performance on correct ratio compared to BP. It indicated that the performance of the proposed model is practically feasible in the application of water quality assessment.