Hello Calais
You need to look at the user manual of telemac3d where everythings are well explained. The answer to your question can take much more than a post on the forum
Just to sum up very briefly, the density variation is taken into account in the momoentum equation as a buoyancy force. this is based on the theory of Boussinesq approximation (mainly, the variation of density is very small compared to the density values itself).
You will have much more details in the J.M. Hervouet book, in the documentation of Telemac-3D or in any good book of free surface hydraulics.
with my kind regards
Riadh