There is and we do.I'm certain if there was a brain eating bacteria, we would have known about it. My best guess is that there were multiple issues that made them decide the cons outweighed the pros. Probably included in that was the rate of growth of the entire resort. When River Country opened, the only hotels that were open were Contemp, Poly and FW. So, a very small population and for all it was quickly accessible by boat.
In the late 80s and 90s, WDW boomed. With both Typhoon Lagoon and Blizzard Beach being open and having more options, and being more easily accessible to more people, I'm sure River Country became less populated, less in demand, and more of a hassle to keep up.
Plus, in this time period you've got the ADA that came out, and several other rules and regulations for safety that just didn't exist before. So at a certain point, I'm sure Disney said it's not worth it. To become compliant would cost a fortune and we won't make the revenue to make it up in the end, so let's call a spade a spade and shut it down.
I miss it, but if there's one thing Disney knows it's how to turn a profit. So, it is what it is.
http://www.kctv5.com/story/25998330/deadly-case-of-brain-eating-amoeba-reported-in-johnson-county
While said brain eating amoeba is one of the main reason you can no longer swim in the lakes at Disney, it was one of a myriad of reasons RC closed.