Hello,
I think we are getting confused in what you really wish to achieve. The TELEMAC system is used in estuary application all the time and we can obviously handle and predict exchanges between the river the sea.
As Jean-Michel said, you should define your estuary with one "level imposed" at the open boundary on the sea side and with one "discharge imposed" at the upstream boundary on the river side.
Ideally:
- the placement of your boundaries should be sufficiently far from you salinity variations; and
- you would like to have a constant salinity on the sea side, and a zero salinity (fresh water) on the river side, i.e. you must have your river boundary upstream of your tidal prism.
On the river side, the discharge is imposed, so you can impose a TRACER to zero. This will simulate fresh water input. Note that you can vary the discharge to represent daily, seasonal, hydrographs.
On the sea side, the level is imposed. However, this does not mean that the TRACER cannot be set. At the contrary, if the tide is rising through an increasing level imposed, TELEMAC will calculate the velocity as entering the domain, and will therefore imposed TRACER concentration to your imposed salinity value. If the tide is dropping through a decreasing level imposed, TELEMAC will calculate the velocity as exiting the domain, and will therefore, in this case only, ignore the imposed TRACER value but just let the water leave the domain based on the TRACER value inside the domain.
To help you further, please have a look at one of the test cases also distributed with TELEMAC, the mersey estuary.
As Jean-Michel said, the access to the entire source code provides you with the mean to program what ever boundary you actually need.
Hope this helps.
Sébastien