This paper presents the application a numerical modeling study to predict the water exchange rate in a semi-closed lagoon in Haomeiliao. The Haomeiliao wetland was located at Chiayi county of Taiwan. Moreover, Haomeiliao Nature Preserve saturate at the southern part of Budai Commercial Harbor. As a sediment deposit result of Bazhang River and Longgong River, this nature preserve habitat creates a large variety of natural resources, which attracts countless numbers of species and vegetation growing at here. Due to the reconstruction of Budai Harbor, extended facilities may affect the contaminant dispersion and water exchange in the estuarine. In order to evaluate the influences, the numerical models including the two-dimensional depth-averaged hydrodynamics model, the dispersion model and the particle-tracking model are used to predict the tidal-induced mixing, transport and water exchange processes. More details about the model's calibration are also verified on situ measurement not only for water deviation and tidal current, but also an overall performance of qualitative agreement was available. Finally, the residence time shows close links to the intensity of tidal current. The result also shows that the extension of Budai harbor will decrease the current velocity in Haomeiliao wetland, which causes negative ability to the tidal exchange quantity. The future goal on this model can be as a basic tool to evaluate the water exchange issues on environment management for estuarine waters.