Hello Giulia,
Please read the TELEMAC-3D user manual, in particular the "Tracer transport" chapter, e.g. the section dedicated to initial conditions, in particular how to work with USER_CONDI3D_TRAC.
Please also have a look of examples how to implement USER_CONDI3D_TRAC subroutine (see V, Viollet, bump_static, lock-exchange, stratif_wind, tidal_flats, stratification e.g.).
Moreover, have a look at keyword DENSITY LAW to choose the best law to fit what you want to model in the estuary.
Hope this helps,
Chi-Tuan