It certainly could be water in the gas, and if you use gas/ethanol (E10) you probably want to have the tank pumped out. There are a lot of threads on here about water in fuel problems that are much worse with ethanol because the ethanol attracts and combines with the water. The first thing to check is to remove your fuel filter (being careful not to spill any fuel in the bilge) and pour its contents into a clear container. You will see if there is both water and gas in the filter because water will settle to the bottom.
My 2000 Horizon 240 got water in the gas because of a missing O-ring under the gas fill cap. Mine has the vent integrated into the same gas cap. The vent blocks rain water from coming in, but the missing O-ring allowed water to come in around the threaded portion of the gas cap.
Here is a thread about that:
http://www.smwebhead.com/phpBB3/viewtopic.php?f=3&t=9901Of course, there are other things which could cause this stalling besides water in the gas. An ignition system problem could cause the same symptoms, and could explain why it running the bilge pump affected the engine? Perhaps a bad ground or positive connection? A loose power connection going up to the console and ignition switch?
I'll leave it up to others to suggest what to check there.
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"Knot Easy" 2000 Horizon 240 Volvo 5.7GS /SX
tow: 2017 Honda PILOT EXL-AWD
prev. boats:
'87 Chaparral 198CXL 4.3 OMC Cobra
'69 Jetstar 16ft Ski Boat, 115hp Yamaha
'68 Aluminum Jon Boat, 3hp Sears
'64 Water Wings