Mudkip is based on a mudskipper, at least in part. And I'm pretty sure Totodile is just a small crocodile.
But the pattern seems to be animals that can live and move on both land and water. Turtles, crocodiles, mudskippers, penguins, otters, frogs. I don't think there's any pattern beyond that. They just wanted to give you an animal that made sense for a Water-type, but that wouldn't be out of place on land (like a fish would).