It's my understanding that the River Country water was separated from the Bay Lake water by a barrier under the Bay Bridge. See
http://www.talkdisney.com/maps/WDW_River_Country.jpg
In any case, it would not be difficult to keep the River Country water separate from the Bay Lake Water, just as the water at Stormalong Bay at YC/BC/BCV is separate from the water of Crescent Lake.
By now, the aging and and long-shuttered River Country would require substantial work before it could be reopened.
I could see a DVC resort at Fort Wilderness. And I could then see a rebuilt version of River Country serving the same role that Stormalong Bay does for YC/BC/BCV — in other words, as an exclusive super-pool for guests of Fort Wilderness and Fort Wilderness Villas.