There is no alternative to the world’s water resources, and their increasing scarcity is making it difficult to meet the world population’s water needs. This paper presents a sustainable water resources system (SWRS) and analyzes the operating mechanism that makes it possible to evaluate the status of such a system. A SWRS can be described as a complex coupling system that integrates water resources, social, economic and ecological systems into a whole. The SWRS’s operating mechanism is composed of dynamic, resistance and coordination components, and it interacts with and controls the system’s evolution process. The study introduces a new approach, set pair analysis theory, to measure the state of a SWRS, and an evaluation index system is established using the subsystems and operating mechanism of a SWRS. The evaluation index system is separated into three levels (goal level, criteria level and index level) and divides the index standard into five grades. An evaluation model of the SWRS based on set pair analysis theory is constructed, and an example of SWRS evaluation in Shanghai is presented. The connection degrees of the index in the three levels are calculated, and the connection degree of the goal index is calculated to be 0.342, which classifies the city’s SWRS condition as grade 2. The sustainable use of water resources in the region is determined to be at a relatively adequate level that meets the requirements of sustainable development.