The answer is: All of the above!
There's been a lot said about bacteria levels and aligators are a reallity in any Florida water.
WDW is very good about controlling all kinds of reptiles that might detract from our vacations, but they can't keep all of them away all of the time. We were taking a boat out of the Contemporary marina one time and my wife mentioned she just wanted to go out and let her feet dangle in the water. I said that it might not be a good idea. She asked the attendant who was untying the boat if WDW allows alligators in their lake and he just smiled and said, "this IS Florida, ma'am."
So, whether it be bacteria, alligators, snakes, ugly birds, or just plain dirty water, I'll take my chances in the pools where I can see what's going on around my feet.