Two ways of looking at this - Petrols rely on electrics, electrics don't like water, you can mitigate the problem by some waterproofing, but you can't easily submerge the engine! If they swallow water or electrics get wet then they stop and you need to dry them out before restarting.
Mechanical diesels - don't rely so much on electrics, so as long as they can breathe air - and exhaust emissions then they are happy. If however they breathe in any water then the chances are you will do alot of serious engine damage - valves, rods etc... They won't restart necessarily and you could be facing a big bill.
Electronic diesels (TD5 etc.) may also be affected by water in the electronics.
There are merits in either approach. My road car which I use to set up off road events is a diesel and the racer is a V8. I don't take either through really deep water if I can help it as it also can have detrimental effect on all sorts of other parts.