Adam--since no one mentioned it, I have to assume you tried to move the crankshaft with the Compression Release Valve open? If there was water but the crank/cylinders are not frozen by rust, the starter should be able to turn over the crank and expell any water out the valves-- with the compression release open. But if even then you have no movement of the crank, I think somehow the crank is frozen.
There is a tech named Rick at Mack Boring, people in NJ who rebuild the Yanmars. (He did mine is 2009) His phone is (908) 391-1713, and he knows these engines through and through. Maybe he'll take a call from you..just to ask if there are other diagnostics you can do before calling in the Doctor. The number at Mack Boring Co is (800) 622-5364.
I hope you find an easy solution; maybe the Bendix is jammed, and it's a starter problem, that would be a lot easier than water in the engine...
Good luck!
Carl
PS Only once in 30 years was I able to start the 3QM30 using the hand crank, and it took two people--one to turn the handle as hard as possible and another the close the compression valve, at just the right time: as the cranker was pulling up, his strongest point, so he can keep pulling up as the first cylinder compresses. Otherwise the crank is stopped instantly, no joy.