I use Liquitex Acrylic Gel medium. It's perfect if you want to replicate non-smooth water, like bow waves or disturbed brown water (say, for example, a tank entering a stream).
It has the consistency of toothpaste, but dries clear. It doesn't give off any heat as it dries, and the best part is that you can build it up on itself with multiple applications.
Since it dries clear, I usually put an undercolor on the base, most of the time I use the cheap craft paint (like Apple Barrel or Ceramacoat). Once it's dry, apply a wash of color to the surface, let it dry, drybrush any white water you want (like wakes, wave tops) and then clear coat the entire thing with a gloss.
Gel Medium is found in any art supply store, Michaels, AC Moore, etc.
Hope this helps.
Jeff Herne
Modelwarships.com