With the proliferation of ethanol in marine fuel this question comes up frequently these days, and it is tough to get a straight answer. After reviewing the recommendations from two manufacturers, Mercury Marine and Yamaha, I think I can sort this out.
There does seem to be consensus on one thing: if you are going to be storing your boat for more than two months, its best to leave the tank(s) empty. The manufacturers recommend running their proprietary fuel conditioners and stabilizers through the system to clean and coat internal parts. In addition, Yamaha suggests adding their “ring-free” product to the fuel to help clean any gum or tarnish from piston rings and engine internal components.
But it’s not quite that simple. Although the manufacturers seem to prefer draining the fuel tanks, they also realize this may be a major inconvenience due to the hazmat nature of fuel and how much was left in the tank at the end of the boating season.
So, these same manufacturers recommend the following if you can’t get the fuel out of the tank.
1. Top up as needed with fresh fuel, but be careful not to overfill: leave some space for fuel expansion when the weather warms up, as well as enough space for the requisite fuel stabilizers.
2. Add the recommended stabilizers and conditioners in the required amounts for the volume of your tanks. Run the engine long enough to be sure the stabilized fuel gets circulated through the entire system (usually 10-15 minutes).
3. Shut off the fuel valve at your boat’s fuel tank and continue running the engine until it runs out of fuel and shuts down. If you are a bit more mechanically inclined you can drain the carburetor float bowls instead or, in the case of fuel injected engines, drain the vapor separator tank on the engine.
4. Make sure the fuel tanks are not left partially full and do not cap any fuel tank vents. Leaving the tank full will minimize any space for air and minimize condensation, which is how almost all water gets into fuel.