Wartortle: You average Terrapin, just modified to be more bipedal than usual.
Croconaw: Just a larger Crocodile. Some crocs have been known to stand on their hindlegs, but it just didn't suit Croconaw. And if you think it looks a bit like Feraligatr now, you just wait.
Prinplup: Rockhopper Penguin.
Dewott: Otter with a few Beaver features. I made it so the fluffy tufts of fur on its legs were pouches in where it slots in the Scallops.