I hope others are right and some amount of water is staying, but the last time I looked at permits it sure didn't seem that way, other than a tiny sliver alongside the edge of the park where it feeds into the Seven Seas Lagoon, but nothing that guests would even see from the park. I think a great compromise is to keep maybe 20% of the river, dock the boat, and leave it as a scenic sitting/relaxing area. Of course, that wouldn't sell DVC, or LLs, or anything else, and would purely be an investment in the park experience for no monetary gain, so I doubt they do it.