A three-dimensional hydrodynamic model of the lower Columbia River (LCR) was constructed using the Delft3D Flexible Mesh (DFM) modeling suite to simulate water levels, flow, and seabed stresses for time period of January 1, 2017 to April 20, 2020. This data release describes the construction and validation of the model application and provides input files suitable to run the model on Delft3D Flexible Mesh software version 2021.01.