The present study aims to develop a mathematical model for analyzing and predicting the hydrodynamic and water quality in one large lake (Lake Poyang) with great and rapid stage fluctuation, the complex topography and geometry, the complicated connectivity of narrow channels and depressions inside the lake, the frequently switch between exposed grass beach and water.Based on the two-dimensional shallow water equations and pollutant transport equations, the coupled two-dimensional hydrodynamic and pollutant transport model is developed.The unstructured finite volume method is applied to discretize the equations.The nor-mal water mass, momentum and pollutant fluxes are computed by the HLLC solver.The water front moving boundary is identified automatically by the judgment of the latest water stage.It makes the model be capable of simulating the complex flow regime and the dynamic of pollutant transport in the lake with drying and wetting processes.The hydrodynamic model is calibrated by the water regime of the year 1998.Based on the calibrated hydraulic parameters, the hydrodynamic and water quality (COD_Mn and ammo-nia) from January to October in 2008 are simulated by the proposed model.The time series data of measured water stage, COD_Mn and ammonia, and remotely water extent of CBERS data are both used to validate the results of computation in time and space.The results indicate that the model has the capability to model the flows dynamic and the pollutant transport in this kind of lake.