You don't need to keep replacing it just because of the water. Just dump it out and refill it with fuel and screw it back on. Maybe replace it after a couple tanks of fuel. If it keeps running rough, then take it in and get the ecm checked to see if there are any codes.

I guess I wont waste any more money on filters.
the tank is now completely drained and I will take it back out sunday to make sure it was a fuel problem. hopefully.