Numerical modelling has become an important tool in the assessment of riverine systems. Specifically, they can be a useful tool in understanding long-term processes (decades to centuries) and, as such, they play robust and cost-effective roles in supporting engineering planning and design. In this study, a numerical model was developed to simulate long-term sediment transport and morphological evolution for a creek rehabilitation project by using HEC-RAS software. The model effectively incorporated Digital Elevation Model (DEM) data, land use information, sediment survey data and culvert specification. A quasi-unsteady flow approach was used as hydraulic conditions in the modelling and simulated for a 100-year duration. By using a longer-term modelling duration, it allowed longer-term sediment dynamics to be incorporated in the absence of sediment rating curves, rather than assuming equilibrium conditions. The modelling results identified river bed erosion and deposition in the different study reaches as a result of sediment conveyance affected by the culvert structures and allowed insight rehabilitation measures that were appropriate to be adopted during planning stages.