If you are looking at salt intrusion in an estuary where the vertical is well-mixed, then yes: TELEMAC-2D should be sufficient.
There are many ways you can initialise your salinity field:
- the first solution would be to start your simulation with no salt and add salt at your open/offshore boundary. After a few cycles (I would think up to 10 days or so) the salt should naturally have entered your estuary and stabilised to its "natural" state. You can then use the results as a hot-start-file, or PREVIOUS COMPUTATION FILE.
- the second solution, if you already know roughly where the salt is, is to create your hot-start-file with a graphical package, say Blue Kenue. You would have to set WATER DEPTH (or FREE SURFACE), which you can choose constant, VELOCITY U and V and the SALINITY. In Blue Kenue, it is easy to map values to part of your mesh.
Hope this helps,
Sébastien.