Basics
Boats with engines, like cars with motors, run on gasoline. Gasoline nowadays is mixed with ethanol, which is a form of alcohol. Alcohol is hygroscopic, which means it likes to suck in water -- such as moisture from the air inside the fuel tank. Gasoline is a solvent, which means it likes to eat things -- such as at the lining of an idle fuel tank. Gasoline and ethanol together make boat fuel, which like any other fuel has impurities in it; if the impurities aren't burned off in the boat's engine, or cleaned out by the engine's gas filter, they collect in the tank.
Perils
As ethanol absorbs water, it becomes heavier than gasoline, and sinks to the bottom of the fuel tank. That's not a big problem when the boat's moving and the fuel's pumping, but it is troublesome when the boat doesn't move for several months. Then you have a fuel tank with "phase separation" -- a level of gasoline and a separate level of ethanol (which doesn't have enough oomph to run the engine when the owner starts up the vessel in spring). Ethanol and water can be corrosive, too. Problem is, one alternative -- draining the tank -- has its own dangers. Fuel vapor builds up in "empty" tanks, and a stray spark can trigger an explosion. The U.S. Environmental Protection Agency did its own study of phase separation in boat tanks, and concluded that the problem isn't really in the fuel -- it's in the filling station's fuel tanks, which may be full of water.
Solutions
Fill the tank 95 percent full to allow for expansion and contraction to minimize the danger of fuel-vapor explosions, says the National Fire Protection Association. Add fuel stabilizer and conditioner before winter to help prevent fuel separation and stop the fuel lines from gumming up. Small tanks can be emptied, if boat owners then store the boat to avoid fuel-vapor buildup. Try to buy your boat fuel at gas stations away from the ones at marinas, where underground storage tanks have their own water-buildup problems.
Tips
As with storing a car, the fuel system must be checked when storing a boat. Drain fuel filters, examine hoses for leaks and then sample boat fuel in a clean glass jar. If you see black specks, the ethanol is eating away at the hoses; replace them with ethanol-resistant lines. Empty tank or full, the worst solution is a compromise: The half-full tank both sucks in moisture and builds up explosive fumes.