Hello,
The latest version of Telemac-2D (version 7.0) has a first set of simple water quality models. Otherwise, as a matter of fact, you can run Delwaq as a post-processor, with the keyword COUPLING WITH : DELWAQ, it gives, through a number of other keywords, a number of files which can be run with Delwaq, which is also open source. I think there is a test case in the port-folio of examples which shows how to do. The name is delwaq? (I am not at work, not sure...).
With best regards,
Jean-Michel Hervouet