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My thought is either one of 2 possibilities. 1) the fuel cap was loose allowing water in when running no wake zone or slow speeds. Or, 2) you have a bad seal on the cap allowing above scenario.
I know of no other way for water to get into the carb other than through the tank.
 

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The wht bottle on the vent line is a filter/water separator. There is a thumb screw on the bottom to drain it.

If there is that much water in the tank the fuel filter should show it. They are also a water trap by design.

The fuel cap on my GPr is quite high as well. At low speed its often under water riding 2 up especially.
 
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