A more hopeful sign is stratification in the bowl; that is, clear or slightly cloudy water on the bottom and amber liquid on the top. In this case you can probably drain the bad stuff into a bucket, but you still probably have a clogged filter cartridge that needs to be changed (otherwise the engine wouldn’t have stopped), and doing so is considerably more difficult than it sounds. The challenge is to swap the cartridges without introducing air into the fuel system, and the only way to do this is to make sure the cartridge housing is full—and I do mean full—of fuel before you close it back up. And the only way to do that is to extract some clean fuel from a fitting that you can crack open without introducing air into it. (By now you no doubt realize that servicing a separator is something you should learn to do dockside, not at sea.) The good news is that it is highly unlikely you will need to change your main fuel filter (that job is a real bear), since the fuel-water separator has probably protected it.

If you drain your fuel-water separator and change its cartridge and your engine restarts, congratulations. But you’re not out of the woods yet. If it quits within the first couple of minutes, you’ve either got really bad fuel or, more likely, air in the fuel system. The procedure for bleeding a diesel fuel system is engine-specific, but generally it involves cracking a fuel line at the highest point (often the number-one injector) and cranking the engine until only fuel—no air—spurts out. (This is yet another procedure you should practice while you’re tied to the dock.) If you’ve got two engines, you should leave one running, because otherwise you are likely to drain your cranking batteries trying to get all of the air out.

Fuel-water separators come in many sizes and may be combined in two or even threes. Yet they’re simple—no moving parts. Basically there’s just vanes at the bottom that spin the fuel to separate out the water and an efficient particulate filter on top.

And by the way, if you do have two engines and one continues to run, ask yourself why. If both engines draw from a common tank but only one is actually sick, chances are the problem is with the sick engine, not with the fuel. If you have multiple tanks, this would be a good time to move all those fuel-manifold levers around so that both engines draw off the tank feeding the running engine, on the assumption that the fuel in it is clean. You do know how to change the supply and return feeds, right?

Every owner should know how to diagnose and solve a fuel problem—unless he or she is not averse to being at the wrong end of a tow line. It’s not that hard. The trick is to practice the procedure before you are dead in the water.

This article originally appeared in the April 2007 issue of Power & Motoryacht magazine.