Just my $0.02 worth. If the oil doesn't leak out, how is the water supposed to get in there. Sure some is likely to get in the breather holes, but in my experience it's minimal (and usually evaporates back out again). Air has moisture in it. Either the color of the oil will tip you off or the rise in fluid levels if there is much water in the fluids. If the motor and most of the vehicle sits submerged for an extended period of time, more water is likely to seep in.
I grease everything and clean out my brakes. Check the fluids.
Motor can mess up, usually happens when the motor starts missing and somebody just won't say die and shut it down. They either try to keep it running or crank it till it dies. Or drive into the water at high RPM's and the motor gets damaged before it has a chance to stall.
Like mentioned, pull the plugs and crank it over. Look in the spark plug holes with a flashlight.
I keep a couple of cans of ether around, to help get me going again and use it to spray a few spoonfuls into the cylinders (spark plug holes) then crank it over to help move any grit out (disconnect the coil leads, keep a fire extinguisher handy).
I've found the biggest pain, is to wash all the mud out, it gets in places you can't really see and causes problems years down the road. Finding and cleaning all the connectors (WD-40 isn't the best solution for connectors, but does work well in the distributor). I've found near boiling water to be the best cleaner, washes the mud film off and then heats up the connector enough that most moisture evaporates, then a shot of air.
Starter and alternator get coated on the inside with a film of mud (dried dirty water).
I keep a set of junkyard sensors, starter and alternator. Swap it out and clean up the old set for next time.
I've found bottomless mud puddles on numerous occasions, in the last 200,000 miles, haven't swapped a motor out yet. Though I did bend a valve once.
I do pressure wash, mud sand and grit away from most all the seals and the brakse front and rear, sand will eat them up quick.