Hello,
Christophe is right, you must use the latest release before asking for help because some bugs may have been solved + new features may improve the results between releases and we do not waste time for old releases.
Christophe is also right if you know if a thermocline exists, you should refine your vertical mesh around it with a Z-layer distribution (or an hybrid transformation sigma-Z). But you will have to implement your distribution in the USER_MESH_TRANSF subroutine (in release 8.1).
You can try to use MESH TRANSFORMATION = 2 or 5, but not sure it will give better results.
Please read the TELEMAC-3D user manual for release 8.1 to see what to do for the mesh transformation:
wiki.opentelemac.org/doku.php?id=documentation_v8p1r1
Hope this helps,
Chi-Tuan