Hi there,
As you may know, salinity stratification generally results when you have mixing (or lack thereof) of waters with different salt content (e.g. freshwater overflowing seawater), or where you have large evaporative fluxes. Although I have not seen your boundary conditions file, you appear to be prescribing salinities corresponding to freshwater throughout the water column at both ends of your domain, which is not consistent with what you are trying to simulate (i.e., in order for stratification to develop, you will need saltwater to leave the domain through at least one boundary, which will then have a non-zero concentration somewhere over the depth). Maybe try prescribing 10 g/l at one end of your domain.
Enda