The Cruise itself isn’t a part of any natural swamp or waterway (or any of the wet rides, for that matter), being basically a concrete-lined canal. I doubt it supports anything much larger than bacterial fauna, but you certainly woulnd’t want to go for a dip.
When I was there last, the Disneyland Jungle Cruise had been drained for repairs. It looked about 4 feet deep with a single rail track in the middle that the boats are somehow attached to.
From what I read the boats do float but they have a sort of foot sticking down between the guide rails for pathing. I’ll also bet some parts could be deeper to accommodate animatronic hydraulics (based on what I know of the old Jaws ride at Universal Studios Orlando).
There is at least one video of an alligator being removed from Splash Mountain (that’s a man made waterway) and I’ve seen numerous reports of snakes in the parks. I personally have seen 'gators and snakes in the parks.
I wasn’t claiming it to be totally safe. Plenty of nasty bacteria out there.
A gator of significant size in one of the rides is fairly rare. That said, be cautious banks of the Seven Seas Lagoon (that artificial lake between MK and the TTC which multiple resorts like the Grand Vic and the Poly border on) - a toddler got killed there a few years ago by a nine footer, and a few small dogs have been attacked over the years as well.
Admittedly, I wasn’t thinking about snakes. You’re somewhat more likely to come across cottonmouth for example but the rides don’t really support the fish and frogs such snakes mostly eat. Venomous snake bite cases are pretty low on property for all the millions of annual guests.
Our family was on one of the Jungle Cruise boats at Disneyland when it became stuck on the track and wouldn’t move. They had to send another boat to pick us up. We shouted, “Boarding Party!” as we hopped over the gunwales like Crimson Pirates. I thought about growling, “And them that dies’ll be the lucky ones!” Stern looks were our reward. Aaaarrhh.
There can honestly be alligators anywhere in central Florida. Plenty of people with wet weather ponds that only fill when it rains have gone out after the rain to find a gator. It’s less likely since it’s not directly connected to a waterway, but could still happen.
As I said on one of the other posts, it can happen but you aren’t likely to see one within the ride that is large enough to be dangerous - Reedy Creek would get called in to scoop them up fairly quickly. As I also said, the bodies of water across the wider resort property is a different matter. Lot more acreage to cover and open ways for animals to move in. Incidents have happened.
BTW, I do have some idea of what goes on around there. Before moving across the country I spent most of my life in central Florida and was even a WDW cast member (entertainment) for several years.
Chlorine on its own doesn’t smell. It’s the chemical reaction between chlorine and pee that gives off what most people assume to be a chlorine smell. The worse the smell the more pee. Think of that next time you’re in a hotel swimming pool.