This isn't what you asked, but I will note that if you don't have experience with hydrodynamic modelling, or access to somebody who does, then the use of these models may have a steep and time-consuming learning curve.
The most up-to-date version of the sediment transport module is part of the Coupled Ocean – Atmosphere – Wave – Sediment Transport (COAWST) modeling system. A good description of the model and its capabilities is given in Warner et al. (2010). The code can be downloaded from here.
The current version of CSTMS can model both cohesive (mud) and non-cohesive sediment (sand) sediments, bedload transport and sediment deposition and erosion caused by waves and currents.