Sounds like you do have a pin hole in the exhaust manifold.All it takes is a pin hole to push water into a cyl on the intake stroke!You can buy just one side to replace,but its just a matter of time the other will do the same.How old are they?Fresh water break them down too!Is the engine FWC?Replace them with a good set of Osco manifolds and risers.Cost around $400-$450.To help installing them,find a after market one piece exhaust gasket.It doesn't have to be marine to use it in that gasket.Have you pumped some engine oil into that cyl?If not do so now.If and when you pull that manifold off,bunp the engine till the piston is just about all the way up,shine a flashlight in the plug hole,see if you have any pitting on top of the piston if you don't want to pull the head.Water injustion normal just wipes out a piston top if it is just a little water at a time or bends the push rod were it wipes out the engine complety were it takes out that cyl and piston all together.You would of known if that happen at the time the engine quit running.Its not nice if the later happen.
Forgot,what baitkiller said about the clean trail will tell the tail.Good one Baitkiller!