I have not done this before, but this wiki page describes the process:

http://www.cequalw2wiki.com/First-time_Users:First-time_Users

Good luck.

first you need section profile for each segment of your water body

then you can export elevation and width of each layer from these profile.

this data can import by input file editor in ce-qual-w2 or by editing a sample file in w2control program.

hope it help :)

oh I forgot to add you can use this software too  : "Watershed Modeling System (WMS)"

Dear P.Saeidi and G.Roemer many thanks. They were all useful. :)