I'm assuming you haven't started it yet... If you haven't... DON'T!!!. Water doesn't compress..you will bend rods or screw up the head. Any attempt to start the engine may cause more damage. You must realize, the engine might be blown already...I hope not, but it's possible.
First, I strongly suggest you let the dealer take care of this...if water got in the cylinders, you could do some serious damge up to destroying the engine. If you follow the instructions below, you will void your warranty and may do more damage....so, again... LET THE DEALER FIX THIS!!!
Drain the oil...if you can drop the oil pan, do that. Make sure you get as much water out of the engine as you can. Use a new oil filter and replace the oil.
Pull all the injectors. Mark them so you know which ones go where (otherwise, you mught throw the engine out of time. Remove the glow plugs too.
Crank the engine. It is preferable to do this by hand (use a socket on the fan pulley nut). With the injectors and glow plugs out, it should turn pretty easily with a 2 foot breaker bar. If it doesn't, there may be a bent rod. Don't go any further...take it to the dealer.
If water pumps out of the injector/glow plug holes, keep going until you get as much out as possible. This is a good time to drain any fuel in the system to remove any water that may still be in there.
Re-install the glow plugs and injectors and any other parts of the fuel system that were removed.
Now, you can try and start the engine. If you hear any loud clanking noises... STOP!. There is a potential of bent rods now.
Drain ALL other fluids. That means ALL other fluids. Water could have got in through any vent holes, so all lubricants must now be considered contaminated. Replace all fluids and filters. If you wish, you can blow out the system using LOW PRESSURE AIR 15 PSI MAX).
I don't know how your tractor is insured, but if you took out a loan, you probably had to get it on your home owner's insurance or buy a policy. As long as this incident wasn't purposeful (I'm sure it wasn't), insurance should cover it. Any work you do to attempt a repair may void any insurance claims. I'm sure you feel like an idiot..I know I would...but don't make a bad situation worse!
Good luck