Water in fuel??

[Bad Fish]

Does a 1999 150FFI kick check engine light for water in fuel? What is the best process to flush the system if water is found? I was caught in a bad storm the other day while fishing in the Gulf of Mexico. On the way out the water was gl*** and as I ran the boat back head on into 6 foot seas the engine died and the check engine light came on. While inspecting the water separator I found water in it at alarming quantities. After riding out the weather the engine would eventually fire up and run fine for a few hundred yard and then die out again. I repeated this process until I made it to a no wake zone in which the engine idled fine all the way to the dockage with the check engine light still shining. Any thoughts on this matter would be greatly welcome and appreciated. Will the ECM need to be reset once the water issues are resolved? Thanks for your time and input on this matter!!

Bad Fish

[boats.net]

Yes water in the fuel can cause the engine light to come on. You can suck the water from the fuel pick-up tube till nothing but fuel comes through. You should also have the computer diagnosed by a dealer just to be sure there are no other problems.