As components of a large‐scale ecosystem restoration project, three intertidal lagoons are proposed offline of the Frog Creek and Terra Ceia River (Frog Creek System, Florida), which are mangrove‐covered and micro‐tidal estuaries. A three‐dimensional hydrodynamic model has been developed based on EFDC (Environmental Fluid Dynamics Code) and the effects of proposed lagoons on short‐time‐scale salinity variations have been evaluated. High resolution airborne LiDAR data is employed to depict the bathymetry of mangrove areas. The model has been calibrated and verified by using water level and salinity observations. Due to the proposed engineered lagoons, the tidal prism will be changed and the following conclusions have been obtained from the numerical experiments. (1) The effect of three engineered lagoons is insignificant under low, moderate and super high inflow conditions and the high inflow condition has the most significant effect on salinity regime. (2) In upstream areas, the salinity is increased because the lagoons will import more saline water. In downstream areas, the salinities with and without lagoons are almost the same during flood tide. However, the surface salinity with lagoons is larger than that without lagoons during ebb tide. (3) In downstream areas, the absolute differences between surface salinities with and without lagoons are larger than those of bottom salinities. On the contrary, the absolute differences of bottom salinities are larger than those of surface salinities in upstream areas. It is of great importance to evaluate reasonably the influence of human activities or natural changes on surrounding environments; and this model can serve as a powerful tool in wetland analysis.