The problems of salinization, organic pollution and eutrophication are very severe in the Wuliangsuhai Lake. In this paper, a coupled model was built based on Environmental Fluid Dynamics Code (EFDC) model and three-dimensional eutrophication (CE-QUAL-ICM) model, with considering the various meteorological factors and the form indicators of emergent plants (e.g. density, height, diameter etc),. This model can reasonably reflect the effects of absorption and degradation of polluting substances by aquatic plants, the bottom stress change and the flow field change. Then the coupled model was applied to predict the inter-annual and seasonal changes of algae, total nitrogen, total phosphorus and chemical oxygen demand with different scenarios in the Wuliangsuhai Lake. Results indicated that the model can well describe the inter-annual and seasonal changes of water quality model when considering the effects of emergent plants. Simulation results were close to the measured ones, with relative error less than 30% and most of absolute error less than 20%. Reducing the pollutant load into the lake directly affected the changes of water quality in the lake. In addition, it is difficult to obtain the information of water quality in water area with shallow and dense emergent plants. However, the use of the coupled model can solve this problem and provide the basis for reasonable planning and management in these areas.