Dear Ben Kreitner; Here are few links which will be useful to you.

Thanks

https://dl.sciencesocieties.org/publications/jeq/abstracts/19/2/JEQ0190020215

http://onlinelibrary.wiley.com/doi/10.1111/j.1752-1688.1998.tb05961.x/full

https://dl.sciencesocieties.org/publications/jeq/abstracts/12/4/JEQ0120040558

Ben, the AQUATOX model could be used for this purpose. You don't need detailed spatial resolution, so the linked-segment application would be suitable. Both the fate and the effects of the organic contaminant could be simulated, and you could even model daughter products, if applicable.  See

http://www2.epa.gov/exposure-assessment-models/aquatox

Dick Park

The majority of hydraulic simulation programs should come with a simple AD (advection/dispersion) transport module. Thus if you a just interested in the mixing/dilution and handle it as conservative tracer you can probably take any of them. If you want to simulate the microbial breakdown you will need some more advanced ones (though usually a simple 1st order decay is available in the simple modules). You should also think if you want to go for a simple 1D model system (sequential linking well mixed volumes) or a 2D system (if you need to separate left/right bank on a large river). If you are interested in a commercial package from DHI you can contact me and I can send you more information.

Hi Ben,

If you use CAESAR, keep in mind that the tracer component only tracks contaminant that binds to sediment.

Cheers