Yes, it will. The problem is that ethanol blended fuel has the capacity to absorb way more water then non ethanol blended fuel. This could potentially saturate the fuel/water separater. At that point, fuel stops passing through and water does. This will lead to a poor running engine or one that stalls and will not restart. This can also leave water trapped in the fuel rail, depending on the design. If enough is trapped, it can cause a lean cylinder at the closest injector. This can lead to a burned valve or piston.
Speaking of ethanol in the gas...if you were to store the boat over the winter and the ethanol does absorb some moisture, wouldn't the water separator still catch that moisture once the boat is running?