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Down The Rabbit Hole: Finding Water In A Fuel Tank

Removing water from tank

I want to tell you about an experience that occurred last year that is both an interesting tale of system debugging as well as how a company can take charge when it is above and beyond its direct responsibility. And there is something to be learned from what happened and how it was resolved.

Last April, Laurene and I took our first real trip on Spitfire, our 2007 PDQ 41. Leaving Stuart, Florida, we headed north to Annapolis, a 1,200-mile journey that would give us lots of time to learn the boat and its systems. A new boat can be full of surprises.

A couple of days into it, we discovered water in the port fuel tank when the port engine alarm came on with a warning message about water in the fuel. This happened just as we crossed the entrance of the St. Augustine Inlet on a busy Sunday afternoon with lots of chop from dozens of boats out for a day on the water. It was a surprise to say the least.

Laurene took the helm and we continued at reduced speed while I went into the port engine space and inspected the Racor bowl for water. There was none. So I called Dick Tuschick of Rhumb Line Yacht Sales, a friend very familiar with the PDQ line of power cats. Dick explained the alarm sensor was located on the primary fuel filter mounted on the Yanmar BY2 engine, and that it would be necessary to remove the drain plug at the bottom of that filter. So I shut down the port engine and unscrewed the plug ever so slowly, paper towel in hand, to drain the water out but keep diesel fuel from spilling onto the hot engine block. Why do I have to do this, I wondered, and how is water getting into the on-engine filter after going through the dual Racor 500s? This isn’t supposed to work this way…

It was a question that I would ask the rest of the trip north, as the process of draining water out of this on-engine filter occurred every day from that point on during the next three weeks, sometimes five or six times a day. Why was there water in the tank, how did it get there, and why weren’t the portside dual Racors (now switched to “Both On”) catching the water? The clear bowls had water in them now, but neither bowl was ever full.


When we got to Annapolis, the local Yanmar dealer, Jeff Leitch, brought a portable fuel polisher to the boat and over the course of the day pulled another couple of gallons of water out of the port tank. He also inspected the fuel fill system, its venting, and the tank installation.

The eventual conclusion was that, at some point during the construction or life of the boat, someone had put 4 or 5 gallons of water into the port tank. There was no other explanation, as there are no issues or defects with the fuel system and the fiberglass tanks are not integral so there is no condensation. We did not find any water in the starboard tank, and they are both filled at the same time at the fuel dock. Regardless of how it got there, the water was removed completely.

But the lingering question of how water got past the Racors really bothered me, and my opinion was that it had to be that the Racor 500s were too small for this engine installation, and water was getting past them. There could be no other explanation. And Jeff said it was impossible to get the specs for the engine fuel feed pump to match against the Racor filters. The Yanmar BY engine is manufactured by BMW, then marinized and distributed by Yanmar. Jeff’s techs sent questions up the chain of communication, but we never received any answers or information.

I decided the best course of action would be to remove the dual Racor 500 assemblies and replace them with larger Racors, either dual 900s or 1000s. Based on Bay Shore Marine’s estimate for the costs, I decided to install a single Racor 1000 in each engine space. While the 1000 is overkill for a 260hp diesel application, the expense of switchable dual 900s was hard to justify in a twin-engine boat.

When he installed the Racor 1000s, Nick Starr removed the water alarm sensors from the on-engine filters and installed them on the Racor bowls. We then removed the on-engine primary filters, as they were no longer needed.

As part of the installation, a vacuum gauge was installed on top of each Racor, to show what vacuum existed in the fuel delivery system. These common rail electronic engines demand fuel filtered to 2 microns, so I use 2-micron filter elements. I check these filters every day, and it is simple to change filter elements in such an accessible location. (I have never understood the logic of people who rely on engine-mounted filters. Perhaps it is that I have sat through several dozen fuel system seminars presented by ESI’s fuel expert Alex Marcus.)

When we started up the engines for the first time after the work was complete, we noticed the vacuum gauge on the new Racor 1000 measured 5.5 inches of mercury (inHg) at idle, and we saw this on both starboard and port gauges. How could this be? On every other boat I’ve owned, I would have changed the filter element when it got close to this reading. We tried 10-micron filter elements with no difference and with both engines. I then called a senior engineer who PMM Technical Editor Steve D’Antonio recommended at Racor (in Modesto, California), who confirmed that I should expect about 0.5 inches of mercury with a new 1000 element regardless of micron rating.


I emailed Ted Clements, designer of the PDQ 41, who responded that the system was designed with the full involvement of the Yanmar distributor in Canada. Sadly, both PDQ Yachts and this distributor have gone out of business due to the economic meltdown.

What concerned me here is the documentation for this engine states that the electric fuel feed pump for the Yanmar BY2 engine has a maximum allowable vacuum of only 2.93 inHg. Beyond that is to cause the pump to overwork and shorten its life. The 5.5 inHg measured at the Racor 1000 at idle was about twice the maximum allowed by the fuel feed pump. Wouldn’t that be fun if the pump died and I lost an engine miles offshore or in some remote anchorage!

(One might argue that this automotive engine is not ideal for a marine application. Such a minimal maximum threshold may be fine for a sports sedan but it is not reasonable for a cruising boat with a more complex, multi-tank fuel system. The filters for the 8.1-liter Deere engine on my previous boat, Growler, for instance, needed changing closer to 12 inHg, although that was never approached, thanks to our fuel polishing system.)

Jeff Leitch and I agreed that to be on the safe side, Laurene and I would not go on any long cruises until we figured this out. Something was definitely not right, and there was no point in burning out a pump, knowing it was working beyond its capacity. After much discussion, Mack Boring’s Jon Henkin sent one of his managers, Mike Alfano, and a tech to join Yanmar’s Eric Shaffer for a day of troubleshooting on Spitfire. Toolboxes open, laptop plugged into engine ECMs, and notebooks ready, they methodically checked out the system, isolating each element of the puzzle as they took measurements, took apart hoses, drained then refilled fuel lines, took gauge readings, and made copious notes. It was most fascinating.

I was told no engine damage has been done to my engines, and the issue is now about shortened life of the fuel feed pump rather than a catastrophic engine failure. Electronic engines compensate for the environment they are in.

Mike declined to tell me his diagnosis but said they would take all of this data back to the shop for analysis, and get back to me with a plan. But from their discussion, it seemed clear to me that some combination of length of run from the fuel tank to the fuel pump, the diameter of the fuel hose used, and the rise (vertical height) from the tank to the fuel feed pump created a restrictive fuel delivery system.


Right after Trawler Fest in Baltimore, one of Mack Boring’s top wrenches, Tom Motta, drove up from North Carolina, and Tom fixed the fuel delivery system on Spitfire. After a summer of frustration and a lot of money spent to get to the bottom of this, he was the right guy who made it happen. Period.

Tom spent some time inside the engine spaces, then he sat down and explained what he planned to do, and it was somewhat different than what he had been instructed. But Tom has 30 years in this business, and knew what needed to be done.

He said there was no way Yanmar’s Canadian distributor could have done a proper sea trial on this boat. The issues and potential installation complications were simply too obvious to be missed by a seasoned engine guy. His New Jersey accent gave that statement some authority.

Tom’s plan wasn’t to increase the size of the fuel hose, as he had been told, but rather to install a couple of universal electric fuel pumps, essentially booster pumps for the fuel system. He said that most diesel engines today use electric fuel pumps, and the Carter rotary pump he would install is extensively used across many applications, including Kohler and Westerbeke generator installations.

He said these fuel pumps like to push fuel under pressure rather than pull fuel by vacuum, so he would mount each pump close to the fuel tanks, in spaces that are not likely to ever get wet. On the port side, that is inside the same space as the fuel tank on a bulkhead. On the starboard side, it would go on the bulkhead under the hanging locker floor.

He wired the pumps to come on when the key is turned on for starting the engines, and as the Carter pump pushes fuel at 72gph, they become backup fuel feed pumps.

Tom also added a momentary push-button switch next to each Racor 1000 so I can energize the rotary pump as I look into the bowl at the bottom of the filter, or to refill the Racor both after an element change or when I drain the bowl of particulates or water.

My trip down to Florida this fall was a blast for many reasons, as I met many PMM cruisers out there having fun. Spitfire ran great, and the engines proved powerful, quiet, and economical. And I never had any problem with water in the fuel or other issues with the fuel system.

The specific details of this experience may only be relevant to my boat and the handful of other 41s. And in all fairness, PDQ Yachts was the first builder in North America to use these BY engines, and Yanmar did not have much of a track record with them. It takes some time to learn the application boundaries of a complex piece of machinery.

But I believe there is more to take away from this story. Finding water in one’s fuel is an issue we will all have at some point, and knowing how to deal with it is important for anyone cruising. It is best to know what to do before it happens.


More importantly, however, is that we are reminded of how vital it is to keep one eye focused from a higher and wider perspective. Had I not had the water in my fuel tank, I never would have questioned the fuel system and learned all that I have. At some point down the road I would have to replace an expensive fuel pump or two. We all assume our boats are built properly and that all systems are well engineered, so we don’t question as much as we probably should. Most every boat I’ve spent time on has surprised me in some detail that was missed or questionable. As owners, we shouldn’t get what is called “target fixation” on the problem but keep the bigger picture in mind. Often the problem is only a symptom of something else that is going on, as it was in this case.

The other significant element to this story is how impressively Mack Boring ultimately stepped up to resolve something they had no hand in creating. I went from being alone with a serious but unknown problem on a boat, from a builder and engine distributor no longer in business, to becoming part of a team that got into the dirty details until the real cause was identified and a proper solution developed.

From where I stand, such a high level of customer support is even more important than the product itself, and will be a driving force in my purchases from now on.