Abstract: The application of the traditional gray correlation analysis method to water quality assessment is prone to cause appearance of "disorder" and "reverse order" in grey correlation analysis. To overcome these problems, the traditional method was modified by nondimensionalizing the original data with the standardization method that was less affected by polar value and rewriting the formula of absolute difference into a new one based on the distance from point to area to improve accuracy of the calculation. Meanwhile, in light of the properties of the water of the the Beihengjing River which was seriously polluted by NH₃-N and TN, weights of the indices were adjusted. The application of the modified grey relational analysis method to evaluation of the water quality of the Beihengjing River in Shanghai shows that its results match the reality better than the traditional one and any other conventional methods.