Reckless, you say the carb was full of water, can you give a bit of a description please. Was it in the bowl and if so how full of water? Or was it just water in the throat of the carb? Or did the carb just "show" water damage?
If you were out on the water and the boat was ah rockin the pump could suck some water off the bottom intermittently and still show a "clear of water" check when sitting still. It can happen so diagnosing one thing at a time is NECESSARY.
Check the manifold, if good THEN check the exhaust for syphoning back to the manifold. If water is "syphoning back" you should also see a "rise" in oil level or milky looking oil. If the oil level has risen the water can be sucked off the bottom before mixing with the oil for easier flushing
. If no milky oil do look to a serious pressure check of the manifold.
Dave Neptune