The common system with one secondary and one primary fuel filter does a fine job of cleaning the fuel that enters the injection pump. This works fine until you end up with contaminants in your fuel. As fuel filters get more and more clogged, you find your engine starving for fuel.
As the fuel gets older, or if you pick up a load of bad fuel the filters plug-up more often, necessitating the need for more filter replacements. Also, condensation in your tanks will contaminate your fuel. Condensation causes microorganisms such as bacteria, fungi, yeast, mold, and to a lesser extent algae. You may not notice the problem until you start running in rough seas. At that point the fuel gets stirred up in the tank and either pulls the sediment up from the bottom or mixes the floating water on top into the fuel.
If you see more than traces water in your fuel separator, you have water in your tanks. Not only does this affect the engine and filters, on a boat with steel tanks (ala GB) it will cause rusting inside the tank.
Some people believe that by constantly topping off the tanks, they can avoid condensation problems. That may be true to some extent, but what about the fuel you are putting in the tank? There is no way to ensure that it is moisture free. Also, because tanks have vents, there is theoritcally always a way for moisture to enter the tank.
For this reason, we have one customer installing a permanently installed fuel polishing system on his boat. This system runs on a timer and bypasses the secondary and primary fuel filters. It is used when the boat is at the dock and runs for the estimated time it takes to run all your fuel through the massive filter that is incorportated into the system. It can also be set up to clean fuel while the engine is running. This system uses its own independent fuel pump and continuously pulls fuel from the tank, through the filter, and back to the tank.
This system came in to us in several boxes and after laying out on the bench, we determined that this is not an installation for the average boat owner. There was a PILE of pipe fittings and lots of wiring to do. Plus the unit is pretty big (of course this boat has huge tanks), so you need to have room to install the pump, filter and electrical box. Installation time should probably take 10 – 12 hours including the equipment install, wiring and plumbing. Equipment costs vary depending on what size system you need. For more information on this system, visit the Gulf Coast Filter website.
The bottom line is that running clean fuel means having a cleaner running engine and changing fuel filters less often.