or, Good heavens -- you have to clean EVERYTHING!
I have had this experience with both outboard and diesel engines. I've never had a gas inboard (ex: Atomic 4), so I can't speak to that.
You wouldn't think anything could grow, thrive and even make huge problems in something that seems as noxious to us as diesel fuel, but unfortunately (as the fellow said in JURASSIC PARK) -- life seems to find a way.
There are critters, most typically a type of algae, who think your tank of diesel is heaven on Earth. Unfortunately like all life forms, they reproduce. Unfortunately like all life forms, they also die.
Once they've died, they settle to the bottom or stick to the sides of your tank, where they may make no problems for years. They may not show up as dirt in either of your fuel filters. They may, however, gather in your fuel line.
You may have no awareness of this until something disturbs either your fuel lines or your fuel tank.
I have often said that my experience is not as extensive as many, but I have sailed intensively since I started, and I have had several experiences with dirty diesel fuel. Fortunately for me, the first time it happened, I was on someone else's boat. He had been in a three-day race in early January. Now, sailing off Florida in January can be pretty dicey, because when fronts come through from the North, they often pack a punch. On the East coast, the northern wind pushes against the Gulf Stream, which flows roughly from south to north at a pretty good clip. When the two collide, very large waves (especially for newer sailors like us) can be the result. You want to check the weather carefully before crossing the Gulf Stream any time, but in winter it is often a problem.
On the west coast where I live, we have a different set of problems. We get the same north winds, this time blowing over lots of open, relatively shallow water. A minor front can create 8' waves in the Gulf of Mexico near the shore, with even larger waves further off shore.
But none of this mattered to my friend, who is a master sailor and ardent racer. Nothing stops him, and with his experience he has a solution for everything. One race unfortunately coincided with a stalled front, and winds were high and the waters rough throughout the race. When one of his crew members got so seasick she was dizzy and disoriented, making bad judgment calls and a danger to herself, the rest of the crew simply tied her to the mast so there was no risk of her going overboard.
His boat performed well in the race, but then he had to move his boat from Clearwater back to Gulfport. It was still too rough to go outside without a full crew, so I went up to Clearwater just to keep him company as he brought the boat down via the more sheltered Intracoastal Waterway. This man loves to teach and pointed out a lot of valuable information to me.
Then came the unintended lessons: right as we were about to go under a bridge, his diesel engine died. He steered the boat through the bridge, glided over to the side of the waterway, and put an anchor down. The problem was immediately obvious: both his Racor filter and his engine filter (often called the "secondary" filter) were black with dirt. He put a plastic red Solo-type cup under the Racor and drained the fuel. He passed the cup to me, and I set it on the nearby galley counter. He changed that filter and the engine filter, and we were shortly on our way. About a half an hour later he pulled the boat over again, put the hook down, and checked the filters, which were clogging up again. He has some clear tubing in his fuel system. He looked at the fuel going to the engine, and it seemed clean, so he started her up again. Eventually she sputtered, but we made it back to Gulfport with just one more round of filter changes.
Unfortunately, it's a very bad idea to drain fuel into a Solo cup. Diesel dissolves that kind of plastic, and we had a mess to clean up in the galley. Keep a glass jar (maybe the size spaghetti sauce comes in) with your engine tools, wrapped against breakage, in case you have to drain your Racor filter.
So then the question was "why?" My friend believes that the rough three days of racing sloshed the fuel around with vigor, essentially scrubbing a lot of dirt collected over years of use back into the fuel. Diesel engines are very sensitive to supply interruption. A tiny air bubble can bring it to a stop, which is why your manual explains how to "bleed" the engine of air bubbles. A tiny bit of water can stop it, which is why you should have a Racor-type filter, which catches water as well as dirt. Dirt in the fuel can stop it. This is all because of the way diesel engines work: very small jets spray a very fine mist of fuel through injectors. Because that spray is so fine, the smallest (noncombustible) thing can replace the diesel, depriving the engine of fuel. Gas engines aren't as sensitive to these things as diesels are. My friend got rid of his fuel and cleaned his tanks, and solved the problem, at last for then.
Eventually my friend needed a new engine, and then he suddenly had fuel interruption problems again. He had his tank cleaned, and got rid of the old fuel (if your boat holds a lot of fuel, there are companies that will "polish" it for you and clean it up) -- but the problem persisted. What my friend eventually discovered was that his fuel lines were so clogged with dirt that it didn't matter how clean his fuel and tank were. He replaced those hoses and had no more problems.
Later on, I also had the same problem, again stemming from sailing in rough water, but in spite of my previous experience with my friend, I didn't realize what the problem was at first. All I knew was that the engine would unexpectedly die. The first time it happened, someone suggested that my propeller had caught a piece of line floating in the water and then released it. He said, "Sometimes that happens." When it happened two more times, however, I discounted that theory. I didn't picture a stray rope catching on my propeller *and* spontaneously freeing itself three times. Each time I bled the engine, and each time the engine started up. I was thinking I had a little air leak in the fuel system somewhere, but I took a "wait and see" attitude. Then one evening while taking the boat out for a moonlight sail on the Gulf with friends, she died completely, and bleeding didn't get her going again. Now, on this engine, parts had to be taken off the engine to get at that filter, and the Racor was in an inaccessible place (if your boat is like that -- move it!) I thought I was out of fuel. With no fuel gauge, it can be hard to know when getting fuel is crucial.
At the fuel dock, the boat took only five gallons. That's when it dawned on me -- dirty fuel.
Several days later, a friend climbed down into the very deep lazarette at the back of the boat, we pumped out all the dirty fuel, and he cut a hole in the tank. We started passing him pieces of oil pad. My oil pads are about 24" square, and we cut one into fourths. We passed a piece down to him, and he passed it back up soaked up at least 2 lb. of sludge -- and he had barely begun. What a mess, but it had to be done.
This is a big pile of oil pads, sometimes called "engine diapers," but that is also the correct name for
something else, so at the store I suggest you ask for oil pads. You lay one under your engine to catch
oily drips so they don't go into the bilge. Unless you have a big clean-up, if your engine is running properly,
you should just put one under your engine, check it periodically, and replace as necessary. One may
well last a year or more. The material they are made of absorbs petroleum products but not water,
making them very good for cleaning up small petroleum spills. You can buy them in smaller quantities
and for most people, having three or four on hand is plenty.
I was lucky, and my fuel hoses were OK. We had a fabrication shop make a cover for the hole in the fuel tank, with a diesel-resistant gasket (I had them make me a second one to have on hand just in case something happens to the one I have, since it was custom). Surprisingly, that fabrication was inexpensive.
It was a real hassle to do all of that, but I don't worry about getting caught in rough water now. Think about it -- as I've said before, when the ship hits the fan, turning the engine on and being ready to use it can be a good strategy, especially for newer sailors. You need to be sure your tank isn't all clogged up with gunk.
However, I urge you to check with your engine manufacturer and find out which algae-controlling additive they recommend -- and then use that specific brand (and do use it)! I say to check with the manufacturer because part of my problem was that I just picked something off West Marine's shelf. I knew no anti-algae agent had been in the fuel, so I followed the instructions on the bottle to "shock" the tank by using a larger dose than usual. As it turns out, that can be a very bad idea, because if you have lots of live algae in the tank, they will all die at once, and sink to the bottom, which is where your fuel line picks up its fuel. My problem started when I shocked the fuel with this stuff. When my friend cleaned the tank, he found extra heaps of sludge around the fuel pickup. We had to pass him other tools to clean that area out well.
My Yanmar manual actually states not to use the product I used (sorry but I don't remember the name), so I went to the Yanmar dealer. They showed me exactly what to use and made sure I knew how to use it.
Check both your Racor (a valuable and relatively inexpensive engine protection) and your "secondary" filter (the one built into the engine) periodically as part of sensible routine engine maintenance.
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