Getting the water out can be a real pain. You can elevate the bow and try to pump most out with a fuel pump (connect to fuel bulb) but there will still be some on the bottom of the tank that the fuel pickup can't get. What I have found is you need to shake it up (get water in suspension) by running the boat and catching it in the fuel separators.
Sounds silly but the first place to start is to take the fuel caps off and replace the o-rings if they are even there. Most common way water gets into tanks. It is unlikely water is leaking into tanks other than thru the fill.