A 2D depth-averaged flow-pollutant coupled model based on quad-tree meshes was established to accurately simulate flows in water areas with irregular natural boundaries in this paper. The grids were generated by recursive subdivision about seeding points. A new neighbor-finding algorithm was presented. The governing equations were discretized in collocated conservative variables by using the finite volume method, and the normal flux of mass, momentum and pollutants across the interface between cells were computed by a Godunov-type Flux Difference Splitting (FDS) scheme. The model was applied to simulate flow fields around a groin. The computed values are in agreement with observed data. The results indicate that quad-tree meshes have fine local resolution, high efficiency and easy local refinement. It is clear that the quad-tree grid model can offer gains in efficiency when applied to complex flow domains or strong shear flows. Finally, the model is applied to flow fields and concentration fields simulation in Jiangsu Haizhou Bay. The simulated polluted area is matched well with observations. Therefore, this model can be used to predict flow and concentration fields of actual water area with irregular natural land boundaries.