Quick Facts
| After Every Run | Fresh water flush for 2–5 minutes to displace salt from the membrane |
| Long-Term Storage | Pickle with sodium metabisulphite solution for lay-up >3 weeks |
| Minimum Run Frequency | Weekly when aboard; daily on passage |
| Pre-filter Change | Every 200–300 hours, or when pressure drop exceeds 5 psi |
| Scale Treatment | Citric acid solution circulated through the membrane housing |
| Biological Fouling Treatment | Approved biocide — not bleach, which destroys TFC membranes |
A watermaker that is properly maintained will run for years without major intervention. A watermaker that is neglected — left with salt water in the membrane between runs, stored dry, or subjected to a single contamination event — can fail permanently within a season. The maintenance requirements are not complex, but they are non-negotiable, and the consequences of skipping them offshore are severe: a failed membrane three weeks from the nearest port is a serious problem that a spare pre-filter element cannot fix.
This guide covers the complete maintenance cycle from post-run flushing through long-term storage, including how to recognise the signs of trouble early enough to do something about them.
Why the Fresh Water Flush Is Non-Negotiable
When you shut the watermaker down after a production run, the membrane housing contains high-concentration brine — seawater that has been stripped of approximately two-thirds of its water content and is now significantly more saline than normal seawater. If this brine is left in contact with the membrane, two things happen: dissolved minerals begin to precipitate out of solution and deposit on the membrane surface (scale), and biological organisms that passed through the pre-filter train begin to colonise the warm, nutrient-rich brine environment (biofouling). Both processes degrade membrane performance; both are largely preventable by flushing immediately after shutdown.
The fresh water flush procedure routes tank water back through the membrane housing at low pressure — typically by gravity feed or a small booster pump — for two to five minutes. This displaces the brine with fresh water, dropping the salinity in the housing to near zero and removing the conditions that favour scale precipitation and biological growth. The flush does not sterilise the membrane, and it does not remove established fouling; it prevents fouling from occurring in the first place.
Run the flush after every production run without exception. On a passage where the watermaker runs daily, this means a five-minute procedure each time you shut it down. Systems with automated flush controllers handle this without operator intervention; on manually controlled systems, it requires deliberate discipline.
Pickling for Storage
When the boat is going into lay-up or the watermaker will not be run for more than three weeks, a fresh water flush alone is insufficient. Biological organisms will eventually colonise even a flushed membrane; without the preservative environment of continuous operation or a chemical biostatic agent, biofilm forms and degrades the membrane over weeks to months.
Pickling — soaking the membrane in a sodium metabisulphite (SMBS) solution — is the standard marine industry method for medium to long-term storage. Sodium metabisulphite releases sulphur dioxide in solution, which creates an environment hostile to biological growth without damaging TFC membranes. A 1 percent SMBS solution (10 grams per litre of fresh water) is typical for marine applications; manufacturer specifications vary slightly.
To pickle the system: mix the SMBS solution in a bucket, circulate it through the membrane housing using the low-pressure flush circuit until the housing is filled, then close all valves to contain the solution. The pickling solution typically remains effective for one to three months. For seasonal lay-up of six months or more, the housing should be refilled with fresh solution at the midpoint. Before returning the system to service, flush thoroughly with fresh water to remove all traces of the SMBS solution before any product water enters the drinking tank — the sulphite odour is obvious and it is unpleasant but not dangerous at the concentrations used.
How Often to Run
In active cruising use, the watermaker should run a minimum of once per week when the boat is lived aboard. Weekly operation provides enough fresh water flow through the membrane to prevent biological colonisation and keep seals and pump components in good condition. Daily operation on passage is ideal — it matches production to demand and keeps the system in continuous service.
The worst thing for a watermaker, short of contamination, is intermittent use followed by neglect. A boat that runs the watermaker once a month is more likely to encounter slow membrane fouling than one that runs it daily. If weekly operation is impossible — the boat is on a mooring and rarely visited — the pickle procedure is the right answer for any gap longer than three weeks.
Recognising Membrane Fouling
Membrane fouling presents as two distinct patterns, and distinguishing between them matters because the treatment is different.
Falling production rate with stable or improving TDS typically indicates scale — mineral deposits on the membrane surface that physically restrict water flux without necessarily degrading the membrane's rejection capability. The membrane is still rejecting salt effectively, but less water is passing through per hour. Scale is primarily composed of calcium carbonate, magnesium compounds, and barium sulphate depending on the water chemistry of the operating area. The Mediterranean, with its high mineral content, produces more scale than the open Atlantic; tropical Pacific water is generally cleaner.
Falling production rate with rising TDS indicates either biological fouling that is clogging and degrading the membrane surface, a physical membrane failure (pinhole, delamination), or a bypass leak — brine finding a path around the membrane through a failed O-ring or cracked housing. This pattern requires urgent investigation because a membrane that is passing salt is one that is approaching failure, and water above 500 ppm should not enter the drinking tank.
Track both production rate and TDS at each run. A notebook entry — date, run time, litres produced, TDS reading, pre-filter pressure — takes two minutes and provides the trend data that makes early diagnosis possible.
Membrane Cleaning Chemicals
When fouling is established — the fresh water flush is no longer sufficient to maintain performance — membrane cleaning involves circulating a chemical solution through the housing at low pressure.
For scale (mineral deposits): a citric acid solution at 2 percent concentration (20 grams per litre) is the standard treatment. Citric acid is mild enough not to damage TFC membranes, is widely available (food-grade citric acid powder is carried by many cruisers for cooking), and is effective against most inorganic scale. Circulate the solution through the membrane at low pressure for 30 to 60 minutes, then flush thoroughly with fresh water before returning to service. In severe cases, an overnight soak may be necessary.
For biological fouling: an approved membrane biocide is required — specifically formulated to be compatible with TFC membranes. Common products include sodium bisulphite (used at higher concentrations than the pickling dose) and proprietary biocide concentrates. Bleach (sodium hypochlorite) is absolutely not suitable for TFC membranes and will destroy them on contact. Any product labelled as containing chlorine, bleach, or sodium hypochlorite must never contact the membrane.
Pre-Filter Change Intervals
Pre-filters are consumables and must be changed on schedule regardless of visual appearance. A filter that looks clean may be chemically saturated — particularly the carbon block, which adsorbs chlorine and organic compounds invisibly until it is fully loaded, at which point it passes contaminants straight through to the membrane.
The general guideline is 200 to 300 operating hours per filter set, or whenever the pressure differential across the pre-filter train exceeds 5 psi. In practice, the pressure-drop criterion often triggers first in harbours with turbid water; the hour-based criterion is more relevant for offshore use in clean water. Carry a minimum of two complete pre-filter sets — enough for a full ocean passage plus a contingency — and replace on schedule rather than waiting for performance to degrade.
High-Pressure Pump Maintenance
The high-pressure pump requires periodic seal replacement — the exact interval depends on the pump design, but most manufacturers specify seal replacement every 500 to 1,000 operating hours. Pump seals are inexpensive compared to the pump assembly; a seal kit costs $30 to $80 and replacing seals on schedule prevents the more expensive failure mode of scored pump cylinders or damaged pistons.
Signs of impending seal failure include: water weeping from the pump body (pressure-side seals failing), air in the product water (low-pressure side air ingestion), or pump pressure that will not reach the specified operating range despite clean pre-filters and an unobstructed intake. On centrifugal pump designs, impeller condition determines performance — a worn impeller produces lower flow at equivalent power. Impeller inspection is a straightforward job that requires only basic tools and the correct gasket material.
The Catastrophic Mistakes
Some watermaker failures are gradual and manageable. These are the ones that happen instantly and are irreversible without a replacement membrane.
Running in turbid harbour water. Fine sediment in harbour water — stirred up by boat traffic, storm runoff, or dredging operations — will rapidly blind the pre-filter train and, if the filters are changed to keep running, will carry abrasive particles to the membrane. The membrane surface is not resistant to physical abrasion. If the water in your anchorage is visibly cloudy or brown, do not run the watermaker. Wait for the turbidity to clear or move to cleaner water.
Running on chlorinated water. Marina tap water, municipal dock water, and water that has been treated with bleach for tank sanitation all contain chlorine that will permanently damage a TFC membrane on contact. The intake seacock must be closed before connecting to a dock water supply; the fresh water flush circuit must use tank water, not dock water. If there is any possibility of chlorine in the water supply, do not run the watermaker.
Fuel spill contamination. A diesel fuel spill in the bilge, fuel dripping from the fuel fill, or an oily harbour where the intake is drawing surface water all present hydrocarbon contamination risk. The activated carbon block provides some protection against low-level contamination, but a significant oil or fuel spill will saturate the carbon block and pass hydrocarbons to the membrane. Hydrocarbons foul TFC membranes in ways that are not reversible with standard cleaning chemicals. If you suspect fuel contamination of the intake water, shut down immediately.
Offshore Spares Kit
An offshore passage without adequate watermaker spares is a gamble on the membrane making it intact. The minimum spares kit for a blue-water passage should include: a complete set of membrane housing O-rings and end cap seals, two full pre-filter sets (6 elements total for a standard three-stage train), a spare TDS meter and probe (TDS meters are cheap and probes fail from saltwater exposure), a high-pressure pump seal kit, a supply of sodium metabisulphite for pickling, and citric acid for scale cleaning. Membrane seals and O-rings are light and compact; there is no good reason not to carry them.
Some offshore sailors also carry a spare membrane. A 2540 TFC membrane weighs about 2 kilograms and costs $150 to $300 — a fraction of the cost and inconvenience of running without fresh water production for the back half of a Pacific crossing.
Continue Reading
← All Watermaker Guides | Water Conservation →
Frequently Asked Questions
Why is the fresh water flush after every watermaker run non-negotiable? When you shut down after a production run, the membrane housing contains high-concentration brine — seawater stripped of roughly two-thirds of its water content and significantly more saline than normal seawater. Left in contact with the membrane, dissolved minerals precipitate and deposit on the membrane surface (scale), and biological organisms colonise the warm, nutrient-rich brine environment (biofouling). The fresh water flush routes tank water back through the membrane housing at low pressure for 2 to 5 minutes, displacing the brine with fresh water, dropping the salinity to near zero, and removing the conditions that favour scale precipitation and biological growth. Run the flush after every production run without exception.
What is pickling and when is it required for watermaker storage? Pickling is soaking the membrane in a sodium metabisulphite (SMBS) solution for medium to long-term storage. Sodium metabisulphite releases sulphur dioxide in solution, creating an environment hostile to biological growth without damaging TFC membranes. A 1 percent SMBS solution is standard for marine applications. When the boat goes into lay-up or the watermaker will not be run for more than three weeks, a fresh water flush alone is insufficient — biological organisms will eventually colonise even a flushed membrane. Pickling solution remains effective for 1 to 3 months; for seasonal lay-ups of 6 months or more, refill with fresh solution at the midpoint. Flush thoroughly before returning to service so no SMBS enters the drinking tank.
How do you distinguish between scale and biological fouling when watermaker performance declines? Two distinct fouling patterns appear with different diagnostic implications. Falling production rate with stable or improving TDS indicates scale — mineral deposits on the membrane surface that physically restrict water flux without degrading rejection capability. Scale is common in the Mediterranean due to high mineral content. Falling production rate with rising TDS indicates either biological fouling degrading the membrane surface, a physical membrane failure (pinhole or delamination), or a bypass leak through a failed O-ring or cracked housing. Rising TDS requires urgent investigation because a membrane passing salt is approaching failure and water above 500 ppm should not enter the drinking tank. Track both production rate and TDS at each run to diagnose trends early.
What chemicals should and should not be used to clean a watermaker membrane? For scale (mineral deposits), citric acid solution at 2 percent concentration (20 grams per litre) is the standard treatment — mild enough not to damage TFC membranes, effective against most inorganic scale, and widely available as food-grade citric acid powder. Circulate through the membrane at low pressure for 30 to 60 minutes, then flush thoroughly with fresh water. For biological fouling, an approved membrane biocide is required — formulated to be compatible with TFC membranes, typically sodium bisulphite at higher concentrations than the pickling dose. Bleach (sodium hypochlorite) must never contact the membrane and will destroy it on contact. Any product containing chlorine or sodium hypochlorite is absolutely unsuitable for TFC membrane cleaning.
What constitutes the minimum offshore spares kit for a watermaker and why is a spare membrane worth carrying? The minimum offshore spares kit should include: a complete set of membrane housing O-rings and end cap seals, two full pre-filter sets (6 elements total for a standard three-stage train), a spare TDS meter and probe, a high-pressure pump seal kit, sodium metabisulphite for pickling, and citric acid for scale cleaning. Some offshore sailors also carry a spare membrane — a 2540 TFC membrane weighs about 2 kilograms and costs $150 to $300, a fraction of the cost and inconvenience of running without fresh water production for the back half of a Pacific crossing. Membrane O-rings and seals are light and compact; there is no good reason not to carry them on a bluewater passage.