I did something similar up there on my DR350 many years ago. Mine never stopped running, but the end of the muffler was under water and it took 2 4wd 4 wheelers to pull it out.
Mine technically never stopped running while in the water. I killed the motor once I realized I was in deep enough to take in water through the top of the airbox. I just didn't want to hydro-lock that sucker and snap a rod.