Hi Nicolas,
As TELEMAC is open source, you can change everything you want...
In a standard use of TELEMAC, the type of boundary conditions is read in the BOUNDARY CONDITIONS FILE (the first 3 columns as described in the user manuals, for the water depth and the components of velocities). In TELEMAC-2D, these values are stored in LIHBOR, LIUBOR and LIVBOR arrays. But during the simulation, you can change them if you want. Just be carefull if you want to run in parallel...
Hope this helps,
Chi-Tuan