Indonesia owned 23% of all the world mangrove ecosystem. Mangroves have important role in dissipating energy from waves and currents. Hydrodynamics undertaken in this system could encourage sediment deposistion over the short-medium term. It is stabilized coastal morphology by trapping sediments within their root system. Unfortunately most works are discusing on the energy damped by the salt marshes. This study tries to developed the model of the river mouth and vegetated river mouth, biotic-abiotic environment interactions could be more understandable and so does a mechanistic understanding of the tidal routing of water and sediment through mangroves. Recently, methods to solve this are not ready-to use system. To achieve the efficient and applicable model, the robustness and potential of Delft 3D model are applied. Second finding is to make applicable program for practical use in common mangrove vegetation in Indonesia. Third finding is using this as a basis to develop a soft structure like mangrove in detail placing and vegetation type for estuarine conservation.