Typically, the only time this happens is if the vehicle was running when flooded, or was cranked after flooding without flushing the crankcase and leaving the cylinders open.
It was running, as i was driving through it at the time. A van coming the other way caused a wave, which hit the car, which was when it ground to a halt.
If the engine sucked in enough water to arrive at the cylinders as liquid, then the engine is pretty much done. That it runs at all is remarkable. Water cannot be compressed, the piston attempts to compress it, something gives. If you are exceedingly lucky the head- gasket blew out immediately, relieving the pressure before the head, cylinder, piston, injector, glow-plugs or valve(s) cracked. So I suppose it may be worthwhile to investigate the head-gasket.
However, if the engine was merely starved for air and died *before* water got to the cylinders as a liquid, the smoke and rough-running may well be from water in the oil, water in the air intake system and even possibly water in the transmission and the fuel.
Drain the oil, check the transmission fluid (oil), check the water- separator in the fuel system, check the air-filter and start over. Change that oil (assuming some level of success) at about 200 miles as LOTS-O-SLUDGE will be created by this experience. It may even be worthwhile to pull the glow-plugs and squirt some oil into the system and crank it to rinse the oil down the cylinder and through the exhaust valves.
Back in the day (pre-catalyst), it was a relatively common practice to spray a thin stream of water into the air-intake (as from a plant sprayer or similar) and watch large chunks of skunge come out the tailpipe. Never enough to hydrolock the engine, but enough to shock any carbon in the valves and head... and presumably knock it loose. The engine would run very rough during the process, and had to be held at least at 1500 rpm or so. The intended effect was to restore compression on a diesel that had a hard time starting even with good glow-plugs. Many times, it actually worked. You may have gotten such a treatment inadvertently.
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