CE-QUAL-W2 is 2D laterally averaged model (assumes all in horizontal plain is well mixed) Eddy viscosity is a measure of mixing in depth and longitudinal. It varies based on velocity of the system and its length scales, you can find good approximations in these two books for your system:
- River Mixing by Raderford
- Mixing in Inland and Coastal Waters by Hugo Fitscher and others
Other way is you can back calculate that in site based on the velocity of dispersion of a tracer, and then use it into your model.
Thank you dear Kaveh Zamani. By any chance do you know how to modify CE-QUAL-W2 source code? for instance by default the software uses a specific formulation for a phenomenon, What if I want to use another formula?