8 Common Watermaker Problems | Become A Cruiser
8 common watermaker problems

8 Common Watermaker Problems

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Watermakers are installed in so many different locations and positions on boats that two owners of the exact same system may have completely different experiences with their watermakers. One owner may enjoy a hassle-free cruising life where the other is plagued by ongoing problems.

Here are the most common watermaker problems that can pop up on most water maker systems.

Bubbles in the System

It is a common watermaker problem for the o-ring at the top of the seawater inlet strainer to become distorted or damaged when tightening the cup. This causes a leak on the inlet side. Shurflo strainers seem to be the biggest culprits when it comes to this problem.

If the leak is not at the sea strainer inlet it can be at any point up to the low-pressure pump inlet.

The Severity of The Problem

Bubbles in a watermaker system is a serious problem as bubbles passing from 800 psi to 15 psi can expand rapidly and blow out the membrane.


Make Sure to have a replacement o-ring for the top of the cup on board. When reinstalling the o-ring do not use petroleum grease to lubricate the o-ring as petroleum products will damage the membrane. Only use silicone grease to lubricate the o-ring.

I would also suggest having a complete spare strainer on board as I once accidentally chipped a cup when it was knocked off the edge of a counter while cleaning it. The chip was tiny but I could never get it to seal properly again.

Low-Pressure Boost Pump Overheating

Overheating low-pressure pumps are a common watermaker problem. The low-pressure pump overheats, and the thermal protection in the pump shuts the pump down.

If you are finding that you have a high failure rate of Low-Pressure pumps, overheating of the pump is the most likely cause.

The Severity of The Problem

Apart from the inconvenience of been stuck in a remote anchorage without access to spares. The biggest problem that comes from a failed Low Pressure pump is that unless you have a system with sensors and an auto-shutdown capability the High Pressure pump will be damaged if allowed to run for anything more than a few minutes without adequate head pressure.


The solution is fairly easy, mount a simple computer fan blowing continuously on the pump to cool it down. Lowering the pump temperature will prevent the on-off cycling caused by the thermal protection built into the pump from being activated. And a cooler DC Pump is a happy, longer-lasting pump.

Dry Membrane

Dry watermaker membranes are another fairly common water maker problem. Cruisers often scrounge through boat jumbles, eBay, and other discount sites hoping to save a few bucks off of a replacement membrane. When the inner packaging is opened the membrane is dry. A moist membrane is normal. Dry is bad.

When the organic material that makes up the membrane dries out it cracks and forms holes in the membrane structure rendering the membrane useless.

The only Solution is purchasing a new membrane.

Ruptured Membrane – Sudden Inlet System Blockage

It is not uncommon to ingest a large piece of sea weed, plastic or even a jelly fish. This leads to a sudden drop of pressure in the RO membranes from +/- 800 psi to zero psi which causes the membrane to rupture.

How to Check if You Have a Ruptured Membrane

Once you have cleared the blockage. And you are still experiencing very high PPM readings in your product water. The membrane is most likely ruptured if you are able to get:

. 800 psi
. Correct high-pressure pump flow rate
. No flow from the overpressure discharge valve
. Continued high PPM readings


When the membrane has been ruptured. A replacement membrane is your only solution. To prevent blockages from occurring do not make water in anchorages or at sea when there is any contamination present, including high levels of jellyfish.

Ruptured Membrane – Over Pressurization/ Excess Flow rate

Should you accidentally over-pressurize your system to the point of exceeding the maximum membrane design pressure the membrane will rupture. An immediate drop in water quality and a large rise in the TDS PPM will be evident.

Troubleshoot and resolve the same way as you would for a membrane rupture caused by a blockage above.


Ensure that your HP pressure gauge is functioning correctly, make small slow movements when adjusting the pressure, and most importantly ensure that you have a functioning high-pressure over-pressurization relief valve installed that is set to activate +/- 50 psi before reaching the design pressure for your RO membranes (+/- 1000 psi).

Cracked Membrane Housing End Cap

Another common watermaker problem is cracked watermaker membrane housing end caps. Cracked watermaker end caps are common with watermakers with certain manufacturers that use Delrin and not Aluminium for end caps. Over time the Delrin weakens which causes the end caps to crack.

Symptoms include leaking and the inability to achieve full system pressure. A cracked end cap may be detected by a rapidly decaying quality of output water and an increase in TDS readings.

Solution Replace end caps, preferably with aluminum caps if they are available for your watermaker’s high-pressure RO vessel. It may also be worth exploring the cost and reliability advantages of replacing your system’s high-pressure RO vessels with a pressure vessel that has a more robust design.

Generally, there is no need to stick with the OEM pressure vessel provided that you keep to the same membrane size.

Smelly Water

Usually, the smell is from tiny planktonic creatures that get trapped in the prefilters or even the sea strainer itself. Once these creatures die in the prefilters from lack of oxygen after the watermaker has been shut down. Anaerobic bacteria grow, causing hydrogen sulfide to be released. This is the rotten egg smell that you may smell before when you first turn on the water maker.

If left unchecked this bacteria can move throughout the watermaker system and into the membranes themselves. Hydrogen sulfide gas is able to pass through the membranes. Once the bacterias colonize the membranes you will start to smell the hydrogen sulfide gas (rotten eggs) in the product water.


. Change the pre-filters and thoroughly clean out the filter housings including the top caps where the housing screw into
. Perform an extended freshwater flush of the system. About 5 minutes should do it
. Using food grade Sodium Metabisulfite follow the ‘Pickling’ instructions for your watermaker
. Leave the pickling solution in the watermaker for 24 -48 hours
. Flush the ‘pickling’ solution from the watermaker following your watermaker’s manufacturers instructions
. Make water for an extended time of 2 to 3 hours to make sure you completely eradicate the bacteria from the system
. Perform an extended freshwater flush of the system (+/- 5 minutes)

The only way to make sure you do not get the anaerobic bacteria back in the system is to ensure that there are no creatures left in the prefilters after shutting down. The only way to achieve this is by giving your watermaker a good freshwater flush after every use. 3 Minutes of flushing should be fine unless you have particularly long hose runs.

Note that the 3-minute flush timing starts from the moment that the PPM reading is at or better than the normal product water PPM.

High-Pressure Pump – Low Output Pressure

Low output pressure from the watermaker’s high-pressure pump is normally the result of damage to the plunger pump packaging. The High-Pressure pump requires constant head pressure at the hp pump intake which is provided by the low-pressure pump.

If the pre-filters are allowed to get contaminated and input pressure at the HP pump falls damage will occur. The only way to repair this damage is by overhauling the plunger pump with a packing kit.

Overhauling the packing is fairly straightforward and is part of any watermaker fitted with a piston-type high-pressure pump head’s extended maintenance schedule and will need to be performed approximately once every three years.

Common Watermaker Parts

. 40″ Dow Film Teck Membrane
. Sea Water Strainer
. 10″ Pre-Filter Housing (9.75″ x 2.5″)
. 10″ Filter 5 Micron and 20 Micron
. 10″ Carbon Filter
. Inline TDS Display
. Handheld TDS Meter

If you enjoyed this post please take a look at my other boat maintenance and system tip articles. If you have any questions or comments please feel free to add them to the comments section below.

8 common watermaker problems
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Hi, I’m Nic! Our Family of four have been out cruising since 2016. We have sailed about 15,000nm, almost halfway around the world. We sold everything, took the leap of faith, and bought a 10-year-old Lagoon 380 ex-charter catamaran. We’ve fixed every system on the boat, often more than once. Cruising has been such a wonderful, positive experience for our family that I want to share my tips to help you Become a Cruiser.

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