I don't keep water turtles as pets, but when I have a rescue waiting to be adopted out, I keep it in a bare tub of water. Easier to keep clean that way.
I used to use colored glass pebbles as the substrate for my turtles. But it's getting messier and not that easy to clean. So I remove them all, no more substrate. My razorback and painted turtles seem okay with that as well, since there is fake plant inside, especially for the razorback to hide.