OK this happened to me on my WR250F last weekend so I have been doing the research on it:
1. Remove air filter and squeeze out all the water you can - leave it off. Empty all water/mud from airbox.
2. Open the drain bolt (17mm) on the bottom of the carb - let fuel/water/mud run out, let some tank gas run out too. Replace drain bolt.
3. w/ bike upsidedown remove sparkplug and pump the kickstarter with your hand. Keep eyes away from engine as water n'stuff will come out of the sparkplug hole.
4. Replace spark plug with new & dry one. Kick until bike starts.
5. Replace air filter, tank, shrouds and seat - then ride it home.
... sounds better than what I did to get it started LOL.
- Sean