Just don't go further south than like sarasota if you're planning on going to the beach. I don't think it's bad down here right now, but the water is definitely nicer if you stay north of the SWFL area. They've recently started releasing more water from the okeechobee lake, like they do every summer, and that shit is disgusting.
There's some freshwater springs in the state that are actually pretty cool too, at least from what I've seen in pics. Then again...I'm not sure of the alligator situation in those places. Any freshwater body of water, pond, lake, river, whatever, you can almost guarantee there's an alligator in it somewhere.