Dead in water

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Henner

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I have a 2006 seadoo 180 challenger, it was running great then it started acting up and not wanting to start when we would anchor to swim or eat. Then yesterday it finally would not start. Thought I fouled a plug so I went to change the plugs and found water in 2 of my cylinders and think I fried my starter because it only clicks when I tried to turn it over with the plugs out. I tried jumping the celiniod but it still wouldn’t turn over and the wire is really hot where it bolts to the starter. Any idea what would cause water to get into my cylinder while anchored ?
 
After the boat wouldn't start, did you change the plugs there on the water, or did you tow it in and change them and find the water later? If you towed it, did you clamp off the water inlet to the manifold? If not and you towed at any speed, you may have forced water in through the exhaust manifold.
 
My 180 always starts better cold than it does hot. I had some click click before it would turn over last year, changed the solenoid and it's been fine ever since. I don't know about the water issue though. Is it fresh water or coolant? Perhaps a leaking intercooler?
 
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