In this study, a two-dimensional flow-pollutant coupled model was developed based on a quadtree grid. This model was established to allow the accurate simulation of wind-driven flow in a large-scale shallow lake with irregular natural boundaries when focusing on important small-scale localized flow features. The quadtree grid was created by domain decomposition. The goving equations were solved using the finite volume method, and the normal fluxes of mass, momentum, and pollutants across the interface between cells were computed by means of a Godunov-type Osher scheme. The model was employed to simulate wind-driven flow in a circular basin with non-uniform depth. The computed values were in agreement with analytical data. The results indicate that the quadtree grid has fine local resolution and high efficiency, and is convenient for local refinement. It is clear that the quadtree grid model is effective when applied to complex flow domains. Finally, the model was used to calculate the flow field and concentration field of Taihu Lake, demonstrating its ability to predict the flow and concentration fields in an actual water area with complex geometry.