Suzhou Creek is a seriously polluted tidal river in Shanghai, China. With the development of Shanghai, there is more and more concern over the “blackness and stink” phenomenon of Suzhou Creek. Suzhou Creek Rehabilitation Project was launched in 1998, and the planning investment of the Project Stage I was 8.65 billion yuan (about 1.05 billion US dollars). It is important to predict the effectiveness of the project and to optimize it. In this study, the USEPA's WASP model is employed to establish a water quality model of Suzhou Creek by using data from the Third Trial Low Flow Augmentation on Suzhou Creek in 1999 and other monitoring results. Based on this, Suzhou Creek Rehabilitation Project Stage I is optimized and adjusted, so the actual investment of the Project Stage I is reduced to 6.99 billion yuan. By implementing the Project Stage I, the targets of Stage I have been met, the “blackness and stink” phenomenon of the mainstream was eliminated by the end of 2000, and the ecological system was improved step by step.