Ask the Editors: H2O + Exhaust Pipe = Trouble?
Well, getting water into a cold muffler on a modern ATV can certainly mean trouble, especially if it’s pooled internally to a point where it either blocks exhaust flow entirely or alters the back pressure of escaping gas to the point of significant performance loss.
However most of these signs will be apparent immediately. Namely the machine wouldn’t start at all or if it did, would be running rough and stalling out.
Since you say it started and ran well, we’re hoping you had the presence of mind to let it reach operating temperature, which should be sufficient in vaporizing whatever water remained (some would have been expelled from the pressure of starting the machine up) in the pipe, which would then escape the exhaust as steam.
If you have not done so, it’s probably not a bad idea to do so as soon as possible as water sitting within for an extended period of time will rust the metal internals.