I would have thought the air filter is a little higher than the bottom of your spotties so water shouldn't have been sucked up and into the intake.
If you have water in your cylinders and you turn over the engine you risk a hydraulic lock, which will damage the engine rather badly. To avoid this, do as Blacknav said - pull the glows out and you can safely crank the motor. This should help expel the water.
If you HAVE turned over the engine and it just won't start, then there's got to be some reason for this. Check the fuel primer bulb - squeeze it about 5 or 6 times. It should go hard. Make sure the air cleaner is clean and dry. There's not a lot more that the diesel actually needs to start - air and fuel.
I'd have to wonder if the fuel tank has taken any water in? That could cause problems, because diesel will float on water sending the water straight to the fuel pickup. Water can damage the fuel pump and the injectors. This should set off a water alarm in your dash - I think we need to hear from Tweak'e on this, he'd know.