With the increasing emphasis on the ecology and environment of rivers, the construction of ecological waterway projects has become a development trend in China. In recent years, more and more attention has been paid to the qualitative and quantitative evaluation of the ecological effects of ecological waterway construction. Based on pressure-state-response (PSR) and driver-pressure-state-impact-response (DPSIR) logical frameworks, this paper established a state-pressure-impact-response (SPIR) conceptual model. The model took the river ecology and environment state as the main line, and described the disturbance pressure of the engineering construction on the river state, the impacts of the project on the river comprehensive function, and the positive responses taken in the full lifetime cycle of the project. The analytic hierarchy process (AHP) and fuzzy evaluation model were used to study the changes of the river ecosystem status after suffering from the construction pressure and taking positive responses. Taking the 12.5 m deep water waterway project in the Taicang-Nantong section of the lower reaches of the Yangtze River as an example, the disturbance on the ecology and environment at different stages of the project construction and the effort of relieving the negative impacts of the project on the ecology and environment were evaluated by the health level of the ecosystem. The paper can provide a scientific method for the evaluation of ecological projects in river ecosystems.