A coastal wave, hydrodynamic and sediment transport model was developed and applied for a small port in an estuarine system. The study focused on evaluating the installation of coastal structures at the modular causeway mooring field of the port, aiming to reduce sedimentation, maximize the usable waterway, and mitigate the potential for impact on the wetland adjacent to the mooring area. The model performance on sediment transport and morphology change was demonstrated by the comparison of survey data and model calculations. The modeled current fields support a plausible sediment source concerning the material accretion and channel infilling in the mooring field. The installation of a solid structure, a riprap or a sheet pile, surrounding the mooring field can act as a sediment barrier in the study area, which can reduce current and erosion in the identified sediment source area behind the mooring field and result in less sediment supply to the mooring field and the channel area over built structures.