As long as you didn't get the
engine started with water still in the cylinder and the water wasn't in their long enough cause serious rust should be no problem. Pull the injectors and turn the
engine over to
pump the water out of the cylinder. Drain the filter,
oil, refill, reinstall the injectors and bleed the
fuel system. Try to start the engine. Should fire right up as long as there is no air in the
fuel system. If it runs on all cylinders, run it for a 1/2 hour or more under load to get it good and warm and evaporate any water still in the crankcase. Change the
oil and run the engine again. If the oil stays its usual black icky self every thing should be fine. Might want to run the engine for a lengthy trip on a sail and drain the oil again, just to be safe.
If there is an anti-syphon valve in the
exhaust system, that's probably your cause for the water filling the
muffler and back flooding the engine through whatever valve is open, #4 in this case.