Back in my days as a freelance skipper, fuel problems were foremost among my mechanical worries. Water, debris or microbe contamination often clogs fuel filters only after rough seas stir the tanks, and engine-crippling air leaks might not crop up until a boat is running at cruising speed with the tanks drawn down.
I often ran twin-engine boats, so there was usually one operating engine to crawl out of peril, but a neglected fuel system can kill both engines at once. Take it from me: The metaphorical sinking feeling is downright joyful compared to drifting toward a breaking reef without propulsion.
The thing is, even in well-maintained boats, fuel system issues seem to come up often. Just a little ongoing attention can head off most problems before they leave a boat dead in the water.
Stagnant Fuel
The best advice might be the easiest: “Use your boat,” says A.J. Strauss, a technician and warranty specialist at JAS Marine in Southeast Florida. When fuel sits, oxidation, temperature changes and contamination all break down diesel fuel hydrocarbons and lower cetane ratings—a measurement of combustibility. Hard-starting engines, loss of horsepower vibration, or audible knocks and rattles might result. “Combustion is happening either too soon or too late,” Strauss says.
A more common issue, though, happens as fuel volume expands and contracts with temperature changes. This forces damp air in and out of half-full tanks, and the moisture condenses inside.
“That’s especially true in colder climates with bigger temperature fluctuations,” Strauss says. Bacteria, yeast and fungi—sometimes erroneously called algae—thrive at the intersection of water and fuel. Those microbes build up
filter-clogging debris over time and might create acid that corrodes fuel system components.
Fuel Additives
Frequent boat use keeps fuel fresh and eliminates most troubles, Strauss says. During seasonal storage or dormant
periods, fuel additives can also mitigate issues.
Biobor, ValvTect or similar biocides, if introduced before long-term storage, quell microbe growth. After fuel sits for more than a few months, cetane-boosting additives alleviate hard starts or knocking.
Few yachts operate in temperatures below 20 degrees Fahrenheit that require anti-gelling additives. (Gelled fuel returns to normal as it warms.) Biodiesel blends, however, can gel at significantly warmer temperatures, depending on the plant oils from which they’re derived.
Fills, Vents and Returns
Big problems occur when water enters tanks directly. If water reaches tank pickup tubes and fuel filters, it shuts engines down and can cause serious fuel system damage.
“When you have a lot of water in the tank, more often than not it’s from the deck fill,” Strauss says. “Check the O-ring on the fill cap and look for corrosion that keeps it from making a good seal.” Also inspect tops of tanks for pooled water, particularly around fuel pickup and return fittings and tank gauge senders.
Tank vent hoses should raise up above the vent, and then drop straight down to the tank. If vent lines curl in a 360-degree loop, then diesel that settles in that loop during fueling can’t drain. This blocks airflow and creates a tank vacuum that will stop engines until the vent line clears.
Diesels draw far more fuel than they burn. That extra fuel cools fuel pumps and then passes through a fuel cooler before returning to the tank. Ignoring zincs or neglecting periodic descaling might cause that cooler to leak seawater into fuel or create undue tank temperature fluctuations.
Fuel Filters
Primary fuel filters—the ones closest to fuel tanks—
separate out water and most debris. Some sound an alarm if water gets high, but manual inspection heads off problems sooner.
“Whenever you’re checking your engine oil dipstick, shine a flashlight through the filter bowl and visually check for water or debris,” Strauss says. If the diesel fuel filters don’t have clear bowls, then drain fuel from the valves in filter bottoms into a clear, fuel-resistant container for inspection.
Marine diesel fuel should be golden or reddish, and crystal clear. A few small clumps of debris in the filter bowl is normal, but not more. A milky mix or a distinct line with clear liquid below it marks water in the fuel. Black debris on filter innards indicates microorganisms.
Today’s new engines require cleaner fuel. “Tolerances are a lot tighter to make 30,000 psi fuel pressure in electronic control, common rail fuel systems,” Strauss says.
Not long ago, 30-micron primary filters were common. That’s often down to 10-micron filtration now. Secondary filters, located downstream of the engine’s fuel supply pump, have similarly dropped from around 10-micron screening to as low as 2 microns. Filters that are too coarse can pass debris that harms expensive injection pumps or clogs injectors. Filters that are too fine usually just limit rpm, but continued use can damage fuel systems over time. “Follow manufacturers’ recommendations,” Strauss warns.
Many filter housings include a valve that selects between two filters—essentially, a built-in spare. “That allows you to change a fuel filter underway without breaking into the fuel system,” Strauss says. Double-check that just one filter meets engine specs for adequate flow at full rpm.
Fouled Filters
Clogged filters typically limit engine rpm. Telltale signs usually show in primary filter bowls long before then, but a simple gauge screwed right into filter tops is a sure indicator.
Most of these gauges have two needles: one that rises and falls with fuel vacuum, and a “tattletale” that rises with that needle but stops at the highest reading. Be sure to reset that tattletale and note readings over time.
And while those gauges are helpful, visually inspecting filters and gauges underway at cruising speed, when safe to do so, might also reveal developing problems.
When water or debris contaminate fuel tanks, the best course is to have fuel polished by circulating it through external filters. For badly fouled tanks, call in a pro. Some boats install onboard polishing systems that circulate fuel through filters to remove moderate contamination.
Air Leaks
Diesel engines spray fuel at precisely the right time, so it is ignited by air that’s superheated from piston compression. Even just a bit of air in the fuel system interrupts that process. “More often than not, once you get air in the fuel system, the engine will die,” Strauss says.
Small air leaks might limit engine rpm or cause hunting, which is when engine speed varies continuously by 100 rpm or more. Those tiny air leaks, when they occur before primary fuel filters, might be noticed at idle or cruising speed. “You’ll see little bubbles in the fuel filter bowl,” Strauss says. “That could be a bad line or fitting, or a crack in the pickup tube.”
To avoid problems, inspect fuel lines, and replace hoses and fittings once they show spider cracks or corrosion.
Fuel filter housing gaskets also go bad. “Every time you change a filter, change that gasket,” Strauss says. Lubricate gaskets with a bit of diesel fuel, but don’t use grease or gasket sealant. Defects after the fuel supply pump generally leak fuel out, not air in.
Bleeding Air
If engines become air-bound, reprime them by systematically following fuel from the tank through the engine. “The primary filter needs to be filled all the way to the top,” Strauss says. On boats with a fuel priming pump, crack a fitting or bleed screw. Without a priming pump, close the filter valves before opening the filter, and top it off from a small jug of diesel.
Downstream from primary filters, either the fuel supply pump or secondary filter housing often incorporate some sort of manual priming pump. Crack the nearby bleed screw or banjo fitting while pumping until you see clear fuel flow.
Injection pumps, which feed fuel through rigid metal lines to each cylinder individually, might also incorporate manual pumps or bleed screws. Beyond that, many engines require a few injector lines to be cracked while engaging the starter.
“It’s not safe to crack high-pressure fuel lines in a common rail system,” Strauss warns. Bleeding may still be necessary at the primary and secondary filters, though. “Don’t go beyond the injection pump. Common-rail engines will push air out by themselves.”
Learn to change filters and bleed fuel systems at the dock, rather than while wallowing in rough seas.
Spare Parts
“You want at least two sets of primary filters and one set of secondaries aboard,” Strauss says. “That should get you somewhere that you can correct the problem before getting underway again.”
Be sure those spares are kept clean and dry, and include one or two sets of gaskets and O-rings for the entire primary filter housing.
For most cruisers, Strauss doesn’t see the need for spare injectors. “They’re so expensive now, and if fuel takes out injectors, you’ve got bigger problems,” he says. Mechanical fuel supply pumps tend to be reliable, but Strauss warns to carry spares for some generators: “Those small electric fuel pumps just go bad over time.”
Even with vigilance, fuel problems come up, but seldom without warning signs. Pay attention to your fuel system and heed those signs, or risk experiencing that feeling that wells up as both engines sputter to a stop.
This article originally appeared in the May/June 2025 issue of Passagemaker magazine.
