sea doo water leaking ?

my sea doo has a water leak. I checked it on the lake and observed the two black baffles that are to remove water bringing it in to the engine compartment. It at lease looked that way through the plastic tubing. I further filled the engine compartment up a few inches to check the shaft seal and any place else that water could come out from, nothing was found, not a drop leaked out. If nothing leaks out, then nothing leaks in?? Anyway, the baffles that are to remove the water seem to be the problem. Why would they pull the water in and not out?