In an ideal world, diesel fuel would be pristine from the time it leaves the refinery to the time your injectors force it into your cylinders. Unfortunately, this isn't an ideal world. Fuel is beset by all manner of dangers.
Your primary fuel filter will catch many of these culprits, but it may require frequent changing, especially if you happen to take on a load of badly contaminated fuel. A more elegant solution – and one that is catching on fast – is fuel polishing, which actively cleans your fuel of debris and returns it to the tank in pristine condition.
Diesel fuel is plagued by dirt, rust and asphaltenes, which are soft, tar-like particles (usually less than 2 microns in diameter) that naturally occur in diesel fuel and can settle on the walls of your tanks, fuel lines and filters. Another common problem is water in the tank, which impacts the precision machinery of your fuel pumps and injectors.
Fuel-polishing systems can be relatively straightforward (above) or even pretty detailed (below). 
In fact, things can grow when fuel and water interact. This growth is often called algae, but it really isn't. Algae requires sunlight to grow, and there is obviously no sunlight in your fuel tanks. The growth is actually a microbe that lives in the water and feeds on the diesel fuel. These microbes form colonies that can grow rapidly in warm temperatures. Bits of the colony die or break off, then make their way through your fuel system. They can clog your primary filters and even shut down the engine by starving it of fuel.
Polishing your fuel can eliminate all of these conditions and the problems they cause, and there are several ways to do it. One option is to call in a professional fuel-polishing company. Technicians will show up at your boat, pump out the fuel, circulate it through filters and return it to your tanks. This works well in extreme cases, but if you would like to be more proactive – and more independent – then you may want to consider installing an onboard fuel-polishing system.
THINK TANKAGE
The concept behind onboard fuel polishing is quite simple. An auxiliary fuel pump takes fuel from your tank, circulates it through a fuel filter and then returns it to your tank much cleaner.
Many production boats are starting to offer fuel polishing as standard equipment, and it has become a popular do-it-yourself addition. While cutting into the fuel system is not a job for amateurs, it is a project that many experienced boat owners can do, with careful planning and attention to detail. Remember that, like almost all boat projects, the details can complicate things.
One of the factors to consider in putting together your system is your boat's tankage. Some boats have only a single tank, while others have a series of them, including a day tank to distribute fuel to various engines, generators and diesel-fed accessories.
A good fuel-polishing system has to take into account the number of tanks and allow fuel to transfer from all tanks to the polishing components and back. One advantage of having a flexible system with multiple tanks is that you can segregate fuel as it is taken onboard and polish it before it feeds your engines.
INSTALLATION OPTIONS
There are several choices when it comes to installing a fuel-polishing system. Some are available as pre-fabricated systems, pre-plumbed and ready to install, and some come as kits with all the materials, but you must assemble them. You can also buy components and put together your own setup.
Gulf Coast Filters, for example, can provide kits or pre-assembled units for boats with fuel capacities up to 1,000 gallons. One example is its FPS Deluxe Magnum unit. This is a high-end installation featuring filtration to less than 1 micron using a huge filter that can hold up to a pound of contaminant. It uses a high-capacity Oberdorfer Bronze Gear Pump and comes with a water-detection sensor, vacuum gauge and a 12-hour timer. The unit comes pre-assembled on a ¾-inch polymer backboard. This little beauty will polish 120 gallons per hour! Take out a bank loan, however, as it will set you back $3,995.
Gulf Coast Filters also supplies a variety of other sizes as well as kits. The kits typically include all the valves and fittings required for installation. For example, one popular kit is the GCF-FPS-Deluxe-Kit, recommended for boats with 300 to 500 gallons of fuel tankage. It is rated at 120 gallons per hour and is priced at $2,884, which includes all fittings, filter, gauges, sensors and even the fuel hose. You supply the mounting board and assembly. A smaller kit, designed for vessels with 100 to 300 gallons of diesel tankage, is the GFC-FPS-Kit, priced at $1,661. This, too, is a complete kit, lacking only the mounting board and assembly effort.
While pre-fabricated systems and kits make the job easier, they are definitely not cheap, and it is the cost that drives many boaters to build their own system.
SYSTEM COMPONENTS
Whatever route you choose, the components in most systems are the same, starting with the filter itself. Some system suppliers use standard marine filters, such as Racor, Sierra, Gulf Coast or the like, while others opt for filters used in farm or construction applications.
