Boat Fuel Tanks and Systems Guide - Maintenance and Troubleshooting Tips


Man filling up a boat fuel tank
When it comes to boat fuel tanks and systems, you don’t want to take any chances. Not only is it a flammable material, but you also need to do regular maintenance to reduce the likelihood of your boat motor not starting or running correctly.


Common Boat Fuel System Problems

If you are having problems with your boat’s outboard motor, the fuel system is the first place to start your investigations. Here are some of the more common boat fuel system problems:

Water Build-up

Condensation can be a big problem with fuel tanks. When there isn’t much fuel, the void in the tank draws in air as it expands and contracts. The air contains moisture which condenses in the tank and dilutes the fuel. Once the watered down fuel is pumped into the engine, you can run into performance issues and a costly repair bill. The moisture from condensation can also help fungus and bacteria to grow inside the tank.

This problem is of most concern to boat owners with sealed under-floor tanks because they are hard to drain and expensive to fill.  If you are using ethanol-blended fuel you need to be even more careful because ethanol absorbs water (this is known as being ‘hygroscopic’).

Solution: First check for evidence of water in the fuel and syphon it out. Keep the tank almost full of fuel to reduce the amount of condensation but don’t fill it more than 95% to allow for expansion. Another option is to drain the tank and fill with fuel when you next use the boat. A water-separating filter installed between the tank and motor can keep your engine free of water.  The filters with clear bowls at the bottom allow you to see if water has been extracted from your fuel.   If you have to empty this bowl of water a lot this indicates a problem.

Stale Fuel

Boat fuel can go stale quickly. Very quickly. Within three to four weeks unleaded fuel starts to degrade particularly in warm weather. The degraded fuel can clog the fuel system which is potentially costly to repair. The storage life of petrol in the tank is one month, but it can be extended occasionally by topping up with one-third fresh fuel. The new fuel restores the volatile components that have evaporated.    

Solution: If you don’t plan to take the boat out for two or more months, empty the tank or use a fuel stabiliser which stops the formation of gum and varnish in the fuel and protects from corrosion.

Using Ethanol Mixes & E10 Fuel

Australian legislation imposes a 10% cap on the concentration of fuel ethanol blends, so the ethanol available in Australia, known as ‘E10’, is actually a blend of 90% unleaded petrol and 10% ethanol.

Ethanol-blended fuels are hygroscopic which means they absorb moisture. The water in the tank sinks to the bottom of the tank causing a corrosive slurry. No amount of additives or attempts to re-mix will solve the problem. Boaties often don’t know there is a problem until after they start the engine and are out on the water because the boat is burning the fresh fuel on top. Also, ethanol is a natural cleansing agent, so it can loosen contaminants that have built up in the fuel tank, causing the filter to clog.  It can also dissolve many of the rubber materials found in fuel systems.

Older outboard motors are not designed to take E10 fuel. New two and four-stroke outboard motors can take E10 fuel however many manufacturers, mechanics and fuel companies recommend against using it in boats. Any cost savings obtained by using E10 fuel can be paid out many times over in engine repairs.

Boat Fuel System Troubleshooting

Some boaties will tell you that if you’re having any kind of trouble with your outboard motor, 95% of the time it’s fuel related. Here’s how to troubleshoot common issues and figure out where the problem is:

Dirty Fuel

If there’s any chance that the fuel has become stale or contaminated, drain the fuel from the tank (for example using a siphon jiggler) and replace with fresh fuel to see if that solves your problem.

Replace the Filters

Your fuel filters can get dirty pretty quickly, and should be replaced once a year at least.  If you experience issues with the performance of your engine (such as not starting, power cutting out, power surging etc) try replacing the fuel filter & see if that solves the problem.

Check the Fuel Line

Fuel may not be flowing properly if the line is crimped or collapsed. Check the length of the line to ensure there aren’t any problems.

If fuel is left in the line for some months, the fuel can gum up and turn the residue to varnish particles which are transferred to the motor the next time you turn it on. If you can’t remove this debris from the line with a screwdriver, it may be best to flush or replace the fuel line to save potential damage to your motor.

Check the Fuel Primer Bulb

The fuel primer bulb doesn’t have as long a life as other parts of your fuel system. The bulbs can lose pressure and wear out so replacing the bulb may fix your problem.

Blocked Fuel Tank Vent

A blocked fuel tank vent or snag in the fuel line on larger boats with under-deck fuel tanks could be the cause. Check the fuel line isn’t sagging and causing the fuel to puddle. If your vent has a screen, check it and clean out any debris with a wire brush. If the mesh is corroded, replace it. Check the vent isn’t letting in any water from rain, spray or the hose when cleaning.

How to Maintain Your Boat’s Fuel Systems

Many things can go wrong with your boat’s fuel system so it’s make sure you do regular boat fuel system maintenance, especially at the start of the season when you haven’t taken the boat out for a few months.

·       Look all over the tank for signs of corrosion or cracks

·       Check the fuel lines, priming bulbs and connections for cracks, leaks or kinks

·       Replace old fuel with fresh fuel

·       Drain water from the fuel filter, or potentially replace it altogether

·       Check you have the correct fuel/oil mix for your engine  

If your fuel tank is showing signs of corrosion, replace it with a new fuel tank, so you don’t have any fuel leaking into the boat’s hull.

Drain Fuel from the Engine

You don’t want to leave fuel in the engine lines for more than a week or two. To drain it completely, start the engine (make sure you use a motor flusher if your outboard motor is out of the water so it doesn’t overheat) and disconnect the fuel line. Let the engine idle until it runs out of fuel and stops. Put a small rag under the carburettor, crack the drain bowl screw and wait for the fuel to finish draining. Remove the rag, replace the cover on the motor and it can be left for a few months without any problems.  


Regular cleaning of your fuel tank will stop the build-up of contaminants. Fuel breaks down chemically, resulting in the separation of additives and fuel components. The additives sink to the bottom of the tank creating a thick sludge.

Because fuel is a volatile material, always clean the tank in a well-ventilated area and avoid any sparks. Remove the fuel line, take off the fuel cap and plug any vent piping (make sure the tank is sealed). Place one end of a vinyl tube in the tank, with the other end in the container you are using to capture the old fuel.  Connect an air compressor to the tank and turn it on. Slowly increase the pressure to drain the tank. Ideally, use a wet/dry vacuum to remove the last remaining debris then add fresh fuel. Start the engine and run the fresh fuel through the fuel lines.  You may need to replace the fuel filter if it is clogged with debris.

If you have any queries about techniques or products to clean or detail your boat, contact Boat Accessories Australia on 1300 308 161 or contact us online.
Category: Boating

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