That is indeed weired.
Open water ponds are the main watersource for all my habitats.
Even more weired is that neither me hippos nor my gharials ever had that issue (i have them both since several ingame years).
- also my crocodiles, just checked it, they don't even had any water station
Even if the water would have a cleaniless issue you should get warnings about it, long before dehydration gets mortal.
edit: what Deggial wrote would be an explanation.
While you still need dry land anyway, if you built it in a way that they can't do the physical drinking, thats maybe the problem.
My habitats are all plain and simple.
It shouldn't be that way ofc, i agree that "swimming" should auto-fulfill drinking needs.