A typical sub-region of Baiyangdian Lake is selected as the practical study area, which is characterized by irregular geometry and complex bathymetry. The coupled lattice Boltzmann model for simulating shallow water flow and pollutant transport in two dimensions is set up and applied to it. The wind stress is regarded as the main driven force. The bed friction and the gravitional force relating to bed slops are involved. The simulation results well represent the flow field and the distribution of pollutant concentration under the predominant wind. This study demonstrates that the lattice Blotzmann method possesses the robust capacity to deal with complex boundaries and irregular topography.