Most lakes in Florida don not drain into a river. They are spring or runoff fed.
Tannin is released from decaying plants and turns what would be clear water black. The water is not "dirty" with filth. Its "tanned". Not that you should drink the water,

, but its not sewage either. The river near my house is icky brown because of all of the silt/dirt in the water. Course it used to be much worse, it was multicolored back in the early 70's before the textile plants stopped dumping dyes in the water.
Gators have killed 20 people since the 40s. There were three deaths back in 2006 which is very unusual. I remember three gator attacks on people back in the early 90s. One attack happened when a man said he was cleaning the weeds from his prop. The real story was he wanted to wrestle the gator. He lost the match when the gator bit him. Another man said he fell off his sea wall and the gators attacked him. He may have fallen off the wall but he was standing there feeding the gators which is stupid and illegal. The third attack killed a 10 year old in the Loxahatchee river.
We just happened to kayak down the Loxahatchee after the boy was killed. A trapper was putting in his boat to go get the gator. What was interesting is that this part of the river is very narrow, fairly fast moving, and CLEAR. Our kayaks are around 17 feet long and most of the first part of the 20ish mile trip was "fun" because the boats where kinda too long to make the turns easily in the "river". A few miles down stream we found the gator. I have a fuzzy photo of it somewhere. Maybe 6-8 feet long. Real easy to spot in the clear water. That gator only had a few hours left to live when the trapper would take it out. The river was no more than 20 feet wide. In most places only a 12-24 inches deep. VERY clear water. I don't see how the family of the boy could not see that gator. My guess has always been they were feeding the critter when the attack took place.
Don't go into the water between dusk and dawn. DONT FEED the gators. Gators have a brain the size of a walnut. If a two footed creature is giving them food it might as well be food. Especially if the two footed creature is smaller than them. I have been in area in the Everglades that during the day you see no gators for miles and miles and miles. But at dusk/night if you shine a flashlight on the water you will see dozens and dozens of pairs of red eyes.

One would not last long in that water at night. I saw a gar fish get hit by a gator in this spot. The gar did not die immediately. It started swimming in circles. The gator that hit the gar swam slowly after the fish. Gators from the sawgrass somehow knew of the injured gar and started to swim right at the fish.... It did not last long.
The amoeba links were interesting. They said 20 people have died from the amoeba since 1962 in FLA. 200 world wide. Florida averages 456 drowning deaths a year. We had between 3 and 6 kids that died playing school sports in my area last year. I would much rather swim in a FLA lake than the ocean. The ocean has sharks, jelly fish, Men of war, 'cudda's, sting rays, and worst of all, rip currents. But you do not hear people saying don't go to the ocean beach. A few years ago in NC we had Fisteria bloom that was quite nasty. The Fisteria was in salt water. I'll take a lake over the ocean.
I have read other reports that state the amoeba can be killed with antibiotics. But this is not mentioned in the links.
An average of five people die from rip currents in Florida every year. 12 people have been killed in shark attacks in Florida since 1976. Do you think the media in Florida is going to tell people to stay away from the beach?
The photo of the people in the lake show that they are wading and not swimming. Does WDW signs say don't swim or wade? I can't remember.
Would I go swimming in a lake in Florida. Yep. Used to spend most of the summer swimming in lakes. I know someone that got bit by a shark but not by a gator or a amoeba. Would I swim in a lake at WDW? Nope, WDW says not too.
Later,
Dan