Modeling hydrodynamic processes in a salt marsh system is a challenging task, due to the complexity of topographic features and the scale of such features relative to the overall system size. With growing availability of high-resolution topographic measurements, like LiDAR-derived DEM data, it is increasingly desirable to run a high-resolution model in a large domain and for a long period of time to get trends of sedimentation patterns, morphological change and marsh evolution. However, high spatial resolution poses a big challenge in both computational time and memory storage. Vegetation dynamics in a marsh system needs to be properly taken care of with respect to the vegetation zones and elevation from the mean sea level. The interaction between micro-scale topography and vegetation canopy dominates the overall morphological evolution.