The numerical model Delft3D (developed by Deltares) was developed to evaluate the potential effects of proposed navigation channel deepening and widening in Mobile Harbor, Alabama (AL). The Delft3D model setup requires the input of a merged topographic and bathymetric elevations, a wave climate based on significant wave heights, peak wave period and mean wave direction, and a tidal-time series. The model was validated by comparing model outputs from deterministic runs with observations of water levels and velocities. The validated model was used to simulate scenarios of existing conditions and proposed with-project conditions (for example, channel deepening and widening). Simulations were performed for one year (the year 2010) and ten years, with and without 0.5 meters (m) of sea level rise. Model inputs and outputs in the form of topography and bathymetry for the scenario runs as well as output water levels and velocities for the deterministic runs are provided in this data release. For further information regarding model input generation and visualization of model output topography and bathymetry, refer to USGS Open-File Report 2018-1123.