A very good suite for modeling in coastal areas is MIKE from DHI. It is actually an umbrella of modules most of them interrelated. It is a commercial package, but to my knowledge there is a good discount for universities and research centres. Take a tour here: https://www.mikepoweredbydhi.com/.
I know another package, but I am not familiar with it. It is called X-beach and is open software developed by deltares, see here http://oss.deltares.nl/web/xbeach/.
DHI just released the new version for MIKE 2016. In this new version there is a new morphological model that combines 2D modeling (MIKE 21) with 1D modeling (LITPACK), it is called the Shoreline Model (MIKE 21 SM). The problem with 2D models is that after a while the models become unstable and this quickly adds up to provide unrealistic results. On the other hand, the 1D models cannot accomodate 2D effects, so in many applications they are not useful. The SM models combines the two models to allow for long term realistic morphological modelling. As Takvor mentions, there are discount prices for universities, so you may want to explore more in that direction.
I am using Delft3D for modeling the morphological evolution at estuaries. I think it's a useful and powerful tool to investigate sediment transport and morphological evolution in shallow water regions.
I use the Telemac modeling system (http://www.opentelemac.org/) for my estuarine and near coast studies. I think that it is a complete tool. It has several modules interesting for your studies: Telemac2D and 3D (for the hydrodynamics), SISYPHE (Sediment transport and bed evolution) and TOMAWAC (Wave propagation in coastal areas). They have develop also some Matlab routines to represent the results, and an interesting forum where the most part of the model doubts are answered (it was very useful for me). I also know the Delft3D, and I have some colleagues that work with it, but I never used it.
you should also consider the morphodynamic modelling system with grain-size distribution changes described by Kaczmarek et al. 2004 in Coastal Engineering, Volume 51, Issues 5–6, August 2004, Pages 501-529