Water quality models are important tools to support the optimization of aquatic ecosystem rehabilitation programs and assess their efficiency. Basing on the flow conditions of the Daqinghe River Mouth of the Dianchi Lake, China, two-dimensional water quality model was developed in the research. The hydrodynamics module was numerically solved by the altating direction iteration (ADI) method. The parameters of the water quality module were obtained through the in situ experiments and the lab analyses that were conducted from 2006 to 2007. The model was calibrated and verified by the observation data in 2007. Among the four modelled key variables that were water level, CODcr, NH3-N and PO4-P, the minimum value of the coefficient of determination (CoD) was 0.69, which mean the model performed reasonably well. The developed model was then applied to simulate the water quality changes at the downstream cross-section assuming that the designed restoration programs were implemented. According to the simulated results, the restoration programs could cut down the loads of CODcr and PO4-P about 15%, however, they would have very little effect on the NH3-N removal. Besides, the water quality at the outlet cross-section would be still in class V (3838-02), indicating more measures should be taken to further reduce the loads. The study demonstrated the capability of water quality models to support aquatic ecosystem restorations.