Time is of the essence.
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.
Rod