I doubt seriously that you have water in the cylinders. You would have some pretty serious issues if that was the case.
Just under the plugs is a cover (with SEADOO stamped on it) and under that is the actual cylinder head. Between the two is space for water to go through. I am willing to bet the water is seeping from between the seal between those two pieces.
When you pull the cooling cover off, you will see a big square o-ring and a small round o-ring just around the spark plug. If the plug ring is wasted, it is a safe bet to guess that the big one is too.
I may have been wrong on getting them in a kit. I might have been thinking of the cylinder gasket kit.
Those o-rings will cost you around $3 each for the round ones and $12 for the big square one.