Hydrodynamic models have been widely applied to river and coastal engineering projects. Understanding the hydrodynamic process is a prerequisite to modeling the pollution and sediment transport process. Hydrodynamic models of varying degrees of complexity should be selected appropriately according to the object of study, physical properties of the flow domain and hydrodynamic features. The essential procedure of hydrodynamic simulation is described in this paper. The main problems such as selection of model dimension in physical space, choice of variables, boundary conditions, initialization, design of computational grid, model resolution, parameterization of smaller scale fluctuations and sub-grid scale processes, model calibration and verification are investigated.