I realize this post is YEARS old, but I recently (three days ago) "dropped" my bike into a huge mud puddle (hole really). I have water in EVERYTHING!!! Literally filled the crankcase, the combustion chamber, the air box. You name it, there was water. Its a 2012 KLX250S. I really don't know what to do. I pulled the spark plug and water came out. I pulled the oil fill plug and water POURED out. Should I just take it in? Or can I flush the crap out with a few oil filters and lots of new oil???? HELP!!! PLEASE!!!!

 

Ok- I see you posted more info. Drain all of the oil and remove the oil filter. I would remove the spark plug and crank the engine to purge any water from the cylinder. Spray some fogging oil in the cylinder afterwards so that you don't develop rust in the cylinder.
Most of the problem is going to water contamination rather that dirt so you may be able to flush the crankcase with some kerosene/diesel to get any residual crap out. The carb may need to be cleaned-depends on if if got mud in the float bowl. Good luck and take your time-it's a lot cheaper if you get it clean before it starts grinding metal.