I recommend Finite Element Approach and FEFLOW software . The software compatibility with GIS make it a good option for generating and visualizing water quality maps.
If you do not have a license for FEFLOW, you could also use MODFLOW (i.e., SEAWAT or the new package SWI2) and MT3DMS to determine the location of the saltwater/freshwater interface and simulate salinity concentrations. Then, you can export salinity concentrations from the model and generate contour maps in GIS. I use ArcGIS and MapInfo, but there are several GIS options.