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).
