More info please?
Laze, not quite enough info here, but I'd take a stab at it and say, if it runs good on land without water, then your problem will have something to do with water getting into the combustion chamber. Give more descriptive information for better results..........
Oh, BTW, I thought you said you were a noob, what ever that is, about skis and in your profile, you say your the owner of a 99 GSX RFI. Although that doesn't matter, I was just curious if you were working on two skis.