Growing developments in lake basins in China, have adversely affected, the water quality of lake, in particular, the water bodies of many famous shallow lake are seriously polluted in recent years. Some projects have been built up to improve the water quality, for example, the sewage interception project (i.e. Xiyuan tunnel project) and four sewage treatment plants etc. have been built up in Dianchi Lake. In order to predict and evaluate the effects of projects on the water quality, it is necessary to develop a coupled model system, which should mainly include wind, circulation and water quality parameters. This paper describes the development and application of a coupled modeling system in a shallow lake, which include a 3D micro-meteorology model (3DMM), a 2D hydrodynamic model (2DHM) and a 2D water quality model(2DWM).The coupled modeling system has been applied to predict the ejfects of environmental protection projects on water quality in Dianchi Lake.