This dataset contains the Delft3D model of the intensive site 399 in the Terrebonne Basin along the Mississippi River Delta (MRD) in coastal Louisiana. Simulations cover the Delta-X Spring and Fall deployments in 2021 and include hydrodynamics and sediment transport. All files required to run the simulations are included. The model's output of water velocity and depth-averaged sediment concentrations are provided for both deployments. The dataset includes annual inorganic mass accumulation rates derived through modelling intra-annual variability in water levels and suspended sediment concentrations. The data are provided in netCDF format.