The water parks use the same towels that are used at the resort pools. (The pool towels have a different design to make them distinguishable from the room towels.) I've never felt it was wrong to grab a few of these from the pool to take with us to Typhoon Lagoon or Blizzard Beach instead of spending the money to rent them there.
Also, I've seen them offloading the large carts of towles from a truck at Port Orleans. This leads me to believe there's a central laundry facility for WDW, and that maids at each resort don't wash that resort's own towels.
If that's the case, it wouldn't seem to matter if you dropped resort pool towels into the towel bins at a water park when you're done with them. They're all going to the same washing machines, anyway, so I don't think it's a problem to leave them there instead of carrying wet towels back to the resort.