Based on numerical computation model RMA2 and RMA4 with open source code, finite element meshes representing the study domain are created, then the finite element hydrodynamic and water quality model for Huangpu River is developed and calibrated, and the simulation results are analyzed. This developed hydrodynamic and water quality model is used to analyze the influence of discharged wastewater from planning Wastwater Treatment Plant (WWTP) on Huangpu River’s water quality.