Software for sediment transport modeling
I think the best option for sediment transport modeling is the Community Sediment Transport Modeling System (CSTMS) package that was developed for ROMS. CSTMS was created by a group of sediment transport modelers lead by the USGS. One of the many benefits is that it is open-source and, thus, free. The model was designed for realistic simulations of processes causing sediment transport in the coastal ocean (estuaries, nearshore regions, and the continental shelf). Details on the package and its implementation are found in Warner et al (2008). The people from FVCOM implemented this package.



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.