I am riding in the North East US and we had some rain for a few days. Went riding today and track had a lot of mud. When I washed the mud off my bike I may have gotten some water in the muffler. I didn't point the hose directly at the muffler opening so it would just be some inadvertent water.
About 20 minutes later I tried to start the bike and couldn't get it started, choke on and choke off. I finally flooded it I beleive and gave up. My friend said he noticed some water blowing out the pipe when I tried to start. Nothing major though. I figure to let it sit overnight and dry out then try again tommorow. Should I be concerned about it or will it just dry itself out? What happens if a little water goes down your pipe when you rinse it off? Thanks in advance for your help and suggestions.

crfrdr  

Pull off the muffler and tip it over to get the water out.  If you waited this long it's probably dry by now anyway.  

ok the next day I went to start the bike and couldn't get it started. Turns out it was flooded. So I turned the fuel off and leaned the bike over and drained out as much gas as I could. Then kicked about 15 more times till it tried to run. Eventually it turned over. So I must of flooded it pretty bad. Have any advice on how to avoid flooding the bike? Any on clearing a flood situation?  

If the bike is flooded twist the throttle wide open and kick is a few times. Seems like it would make it worse but is actually allows more air in and less suction created to pull fuel in.  

PDK is right. And plug your exhast when washing. And start the bike after washing just for a min.