A three-dimensional hydrodynamic and sediment transport model application of the mouth of the Columbia River (MCR) was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021) to simulate water levels, flow, waves, and sediment transport for time period of September 22, 2020, to March 10, 2021. The model was used to predict the dispersal of sediment from a submerged, nearshore berm composed of sediment that was dredged from the entrance to the MCR navigation channel and placed on the northern flank of the ebb-tidal delta. This data release describes the development and validation of the model application and provides input files suitable to run the models on D3D software version 4.04.01. These data accompany Stevens and others (2023).