For me, the caimen were swimming pretty deep when they went through. But I have a theory. The water in my habitat is divided by a glass barrier but, when I remove the water the entire expanse of water is removed - meaning the game (and I assume, the caiman) were treating it as one body. I've managed to make the game recognize that the water is two different pools so I'll run the game and see if that helps. It's going to make me re-do a whole bunch of path and ground.
I don't know if you've got a similar set-up, where the water is divided but the game is treating it as one body? I've never had any of my swimmign animals exit the water and go onto land.