This work develops a system dynamic simulation model for free-water surface constructed wetlands, as well as provides appropriate values for the parameters of constructed wetland management. The system dynamic model is calibrated and validated by using data from a 1-year study of a constructed wetland in Tainan of southern Taiwan. Additionally, the major parameters that affect the simulation output are obtained via sensitivity analysis by using generalized likelihood uncertainty estimation (GLUE). A high R 2 and Nash–Sutcliffe coefficient of efficiency between the simulated and measured outflow values indicate that in addition to reproducing the changing trends of dissolved oxygen (DO), 5-day biological oxygen demand (BOD5), total nitrogen (TN), total suspended sediment (TSS), and total phosphorous (TP) concentrations, the model can simulate the variations of DO, BOD5, and TSS. Taken into account the interactions among parameters, the GLUE method successfully obtained the model sensitive parameters from the Monte Carlo parameter sets. Sensitivity analysis results indicate that the parameters of microorganisms are sensitive factors that affect DO, BOD5, and TN, while sediment diameter largely influences TP and TSS. Further elucidating environmental microorganisms would increase the model accuracy and provide a valuable reference for constructed wetland management and design.