To keep the port of Port Arthur operational, the mechanical maintenance dredging is required every 6 months to remove sediment deposition caused by tidal, river flows and currents, or bank erosion from the nearby due to wake wash. The objective of this study is to investigate the cause of the sediment deposition to better manage the dredging events at the port of Port Arthur, Texas. The historical bathymetrical data of the port are analyzed using Geographic Information System (GIS) tools to demonstrate that the sediment deposition in the waterway is mainly caused by hydraulic condition changes, e.g., flooding or drought, although wake wash erosion occurs along the eastern bank. Using the available bathymetry data, flow conditions and dredging data during Hurricane Harvey, a one dimensional unsteady hydrodynamic and sediment transport model using the Hydrologic Engineering Center’s River Analysis System (HEC-RAS) is developed. The advection and dispersion mass transport equation is applied to calculate the total sediment load, which accounted for both cohesive and noncohesive sediment transport processes. The results show that the total sediment deposition is fairly close to the field sediment estimated with the bathymetrical data. The sensitivity analysis indicates that sediment grain size distribution is the key parameter for better model prediction. In addition, both dispersed particle setting velocity and floc settling velocity are applied depending on the sediment concentration. In conclusion, the HEC-RAS model can be a useful tool to assess the sediment deposition in the waterway to better manage future dredging events.