Kalen, I'm not sure about wakeboard boats, but in the performance world water in gas is death! So we run fuel filters and water seperators. In some instances they are a combined unit.
If your having problems with water in your fuel (which is a MAJOR problem, not to be taken lightly)
Definatley install one of these units. There easy to install inline, and you can drain them easily before you run. The Fram one about half way down the page is what I'd get for your application. http://www.rexmar.com/page203.html