The conditions for the positive operation of water conservancy projects are described in this paper. A scientific and effective evaluation index system was established based on frequency analysis, theoretical analysis, and expert consultation. This evaluation index system can be divided into six first-level indices: the degree to which facilities are intact and functionality standards are reached, the status of operation and management funds, the rationality and degree of advancement of the management team structure, the adaptability and rationality of the water conservancy project management system, the degree of automatization and informationization of the management techniques, and the conduciveness of the exterior environment. The weights for evaluation indices were obtained through the analytic hierarchy process method with consideration of the difference between public welfare and profit-oriented water conservancy projects. This study provides a scientific method for evaluating the positive operation of water conservancy projects.