Rain is a normal part of Florida weather, and a little shower won’t close down the water parks. But lightning in the vicinity certainly will! For safety’s sake when there’s a lightning strike nearby, everyone will be ordered out of the water. Also, FYI, at Blizzard Beach when there’s a thunderstorm approaching (but not yet near enough to clear the water), the ski lift will be the first to shut down so that no one gets stuck in the middle. Rain checks are sometimes given, depending upon the time and duration of the storm, but they are not guaranteed.
Have fun and make a splash on your next visit to Disney water parks!