change all the fluids and put in a new plug make sure you pump all the water out of the cylinder before putting in a new plug. also your air filter and carb should be cleaned and probably a good idea to grease all your bearings like in the suspension and wheels those get expensive if they rust. and when you change the fluids make sure you flush the trany with oil as to get all the water and moisture out so the bearings have now chance of becoming rusted.
take out the plug..flip it upside down....(the bike...not the plug) hand crank the kickstarter...make sure all water out of cylinder. spray a little wd 40 into cylinder..(will displace any remaining water and wont let it rust.) let it sit for a while. Replace all fluids...make sure carb in cleaned out. put in fresh gas and let her rip.
Good friend had his KX 80 go through the ice last year...spent 2 days under water. Did what I described above and started 2nd kick :-)
The sooner you get the bike started up again the better off you will be.
The first step is to get any water out of the cylinder so the engine will at least turn over. With a two stroke you will also end up with a lot of water in the crankcase that needs to make its way out before the bike will run. Like Mrmedusa said, turning the bike upside down will allow gravity to help get the water out.
Next you need to make sure you are getting spark. If the ignition system is wet it may be shorting out the spark. WD-40 sprayed into the spark plug boot, CDI box and any wiring you can get to (like the kill switch) can help out a lot (the WD-40 will displace the water).
There is a good chance that the fuel system is fine but if it won't run then you should remove the float bowl from the carburetor to empy it. Drain some gas from the tank into a glass jar and look at it carefully. It will either be all water (the gas floats on top), all gas, or a mix. Repeat until you get nothing but gas in the jar.
Once you do get the bike running warm it up and then change the transmission oil. If the old oil looks like it had water in it then change the oil a second time after you have riden the bike enough to get it up to temperature.
As long as the engine wasn't turning high RPM and sucked water in the intake it will probably be no worse for the wear if you do all this right away. If you let it sit with water in places it doesn't belong bad things will happen.