Hello Yann,
You are right, you may have shallows in your estuary (I cannot see only with the mesh). If you have bottom elevation above 0, the free surface cannot be below.
If you really want to have lower free surface, you can locally change bottom elevation (with USER_CORFON or USER_T3D_CORFON subroutines) but the flow will be locally changed.
Anyway, please read the rules of this forum: use the latest release (currently v8p1r1, v7p2 is 3 years old) and do not double send topics (I deleted the other one).
Hope this helps,
Chi-Tuan