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Just got this ski running again after a looooong hibernation. Runs great on the trailer w/ the hose attached (water exiting the bypass outlet, and from the rear), so we went and put it in the water. After about 10 minutes of idling around, the over temp warning light came on and it started beeping.

Got it back home, hooked the water up to it again, and ran it on the trailer for about 10-15 minutes, no problem. Why would it overheat in the water, but not on the trailer?

Also, does water only exit through the bypass outlet when running water through the flush kit? Because there was no water coming from that outlet when I was idling in the river.

I'm thinking there is a clogged inlet line, but wouldn't the flush kit flush water back through that line?
 

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on my 99 900 it has a tube the get clogged. You can see it form the back. It's a black hose the turns 90 degrees. Take it off from the inside and blow it out.
 
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