The pumps at the gas station are set up to collect the taxes automatically. I know I can keep my receipts for the diesel I buy for my tractor and turn in a form and get that money back (taken off my taxes). I don't because it does not amount to much. I'll bet the same form can be used for boat fuel. I would guess that the amount of gas you buy in a year for your boat would not make the effort worth it.
Here is a link to a website with all the form numbers you need:
Motor Fuel Tax Refund for Off-Road Use
What frosts my XXXXs is that the price at pumps at the marina are always considerably higher than the gas station's and they are not required to collect those taxes. I realize they incur an added expense because they have to have the fuel delivered to the docks, but even so it is a big difference.