What kind of water separating filter are you using and are you using E-10 gas? I redid my 30 old Quadrajet last summer and did not see anything like that inside and I've been using E-10 for years. Suggestion:
see if you can get a hold of a fuel testing kit if you are using e-10 and measure the ethanol content, see if its above 10%...
and, consider switching to the more expensive but better Racor filters with the metal bowl for inboards. They are expensive, the bowl can be a pain to change but they are probably the best fuel filter on the market.
PS have the original Perko gas fill on my boat and you can easily buy new caps for this style, I change them about every 2-3 seasons. Never had water in the tank in this boat and the tank and carb are original.