Engine water-locked
If you flood the engine cylinder(s) with water, the engine would water lock. It would not turn any more. If you do it when it is turning, major damage could (would) occur. Normally, you do it (well, you normally, don’t do it) when the engine is stationary or you are just cranking. Then the chances that you can get away with it are reasonable. You have to remove the water out. The easiest thing, in the Perkins, is to remove the glow plugs (you could remove the injectors, but this is much more involved). This opens all cylinders. You could try turning the engine (by hand), but I would recommend to use a hand pump (Pela) to remove as much water as you could first. Once all cylinders are empty, you can crank the engine using the starter. When you do it protect the glow plugs opening with a rag or two - the water will be shooting across the cabin and make a lot of mess on the starboard wall.
Since this kind of flooding occurs from behind (i.e. from the muffler/exhaust side) you should assume that the muffler and the exhaust hose are full of water. Remove water from there using the hand pump.
Once all of it is done, reassemble all parts, change the oil (potentially twice) and you should be good to go.
Of course, all of the above with fingers crossed all the time that nothing went wrong.