Water in a fuel system means big problems for an internal combustion engine. Even small amounts of water can cause an engine to run rough, or not start at all. Emptying the fuel tank and draining the fuel system is one way to get rid of the water, but for the do-it-yourselfer there may be an easier way.
Purchase a bottle or two of Heet or another isopropyl-alcohol based fuel treatment. These products usually advertise themselves as preventing fuel-line freeze-ups, because they remove the water that can freeze inside a fuel line. Sixteen ounces will be good for about 25 gallons of gasoline or diesel.
Pour into your gas tank the recommended amount. Follow manufacturer's directions and drive your vehicle, which will allow the product to flow into all the areas of your fuel system. At every fill afterwards, pour in a maintenance dose of 8 ounces.
Keep the tank filled to prevent water build-up in your fuel line. Most modern fuels have greater water solubility and may be able to handle small amounts of water. Larger quantities of water may need to be addressed by a professional mechanic.