It is significant to construct eastern route of south-to-north water transfers project for the realization of the rational allocation of water resources in northern China. The first phase of eastern route of south-to-north water transfers project will be completed soon and start to operate. Water quality assessment is an important aspect of the operational management of water transfers project. In this study, the water quality evaluation model is established based on the grey cluster analysis method. The water quality of Yangzhou section of Beijing-Hangzhou Grand Canal which lies in the eastern route of south-to-north water transfers project as a case was studied and the water quality was evaluated using data from 2001 to 2006. The research provides reference for water pollution control and water environmental protection for eastern route of south-to-north water transfer project. The case study demonstrates that the model is effective and can establish a basis for decision-making of water quality evaluation. The evaluation method also can be applied to assess other river water quality of the project.