Monitoring water quality is a subject of ongoing concern and study since water quality is closely related to human life. Although Nemerow index method is widely used in water quality assessment, the artificial threshold setting may lead to some errors. In this study, we improved the traditional Nemerow index method and built a three-dimensional water quality assessment model combined with the modified firefly algorithm (FA). Then, we applied the improved three-dimensional Nemerow index method to evaluate 100 random water samples. Compared with the traditional method, the improved one proved to be more objective, scientific and practical.