The source of the water has to be determined. Is the fuel contaminated when purchased or later due to inclement weather and moisture? If the only external source of entry is through your filler cap with a built in vent, it can be modified or in many cases, replaced with a different design. You only have one or two ports into the tank, so figuring out any moisture entry shouldn't be difficult.

I would use an ethanol fuel additive to your tank on a regular basis. It acts as a dry gas, and not only removes the excess moisture due to the ethanol, but prevents corrosion to any of the aluminum fuel system parts.