Brown and rusty stains on the liner or on the floor of the pool are not dirt and they are not algae — in most cases they are metals from the fill water, most often iron from a well. You can recognise them by the fact that they appear all at once, typically within a few hours of shock disinfection or of raising the pH, and that they are visible under water as a discolouration of the surface rather than as a coating. The solution is always in two phases: first get the free metals out of the water, and only then tackle the stains themselves. The other way round means the stains come back within a week.
Is it metals, algae, or just settled dirt?
Telling them apart matters, because each of those three possibilities is dealt with using a different product, and the wrong intervention usually locks the situation in place. Fortunately it can be done in a few minutes and without a laboratory.
The practical chlorine tablet test. Take a chlorine tablet or a piece of fast-dissolving chlorine and hold it directly against the stain for a few seconds up to a few tens of seconds (on a liner, carefully and briefly, so the material does not bleach). An organic coating — algae, biofilm, leaf residue — will visibly lighten at the point of contact or disappear completely, because the chlorine oxidises it. A metal stain will not change at all, or will even darken: chlorine is an oxidising agent, and an oxidised metal is more strongly coloured than a dissolved one. This test is the quickest dividing line between “chemicals for algae” and “chemicals for metals”.
The touch and brush test. Algae and dirt have substance. They feel slippery or velvety, a brush lifts at least part of them into the water, and after vacuuming the surface is cleaner. A metal stain is part of the surface — it is smooth, the brush just slides over it and nothing comes loose.
The timing test. Algae grow gradually: a shadow in a corner on day one, a continuous coating by day three, and the free chlorine dropping in the meantime. A metal stain appears all at once — the pool was fine in the morning and by the evening, after a shock dose or a dose of soda ash to raise the pH, it is brown. If you have dosed nothing in the last 24 hours and the colour has still spread, look for something organic instead.
The colour test. The shade is a surprisingly reliable clue. Iron produces brown to rusty orange, manganese brownish purple to black, copper blue-green or turquoise. Algae stay in the green and yellow range, and in the case of black algae in the dark grey range, but unlike metals they always change the clarity of the water as well. You will find a detailed guide based on how the water looks in the article Pool water colour as a diagnosis, and an overview of the types of algae in Algae in the pool.
Where metals in pool water come from
There are essentially four sources, and it is worth knowing which one applies to you — prevention looks different for each.
Well and borehole water is by far the most common cause in Central European conditions. Iron and manganese occur in groundwater in a dissolved, divalent form that is colourless — the water from the hose looks perfectly clean. The pool is filled, the water is crystal clear, the owner is pleased. The problem only starts with the first dose of disinfectant. The complete procedure for filling from your own source is covered in the article Well water in your pool, and an overview of the other filling options in Filling a pool: the options.
Corrosion of pipework and steel parts. Iron also gets into the water from galvanised pipework, from the steel frame of an above-ground pool, from bolts, hose clamps and old metal ladders. The typical sign is that the stain starts directly underneath a particular metal component and spreads from there down the wall.
Copper from a heating element or heat exchanger. Both an electric flow-through heater and the heat exchanger of a heat pump have parts made of copper or brass. When the pH drops below roughly 7.0 for a prolonged period, the water becomes corrosive and copper is released from them into the pool. This is the most expensive variant of all — the blue-green stains are only a side symptom here, the main damage is happening to the heating itself.
Copper-based algaecides. Copper algaecides work, but copper does not break down in the water on its own. With repeated “just in case” dosing it accumulates and sooner or later precipitates on the walls, around the jets and on light-coloured ceramics. The most susceptible pools are those where the algaecide is used as a substitute for proper disinfection.
Why the water turns brown precisely after shocking
This is the most common “mystery” in pools filled from a well, and the explanation is purely chemical. Iron in groundwater is in the divalent form, which is dissolved in the water and transparent. A shock dose of chlorine, active oxygen or another oxidising agent converts it into the trivalent form, which cannot dissolve in water. Insoluble particles of iron hydroxide are formed — and that is exactly the “rusty cloud” that appears in the pool within tens of minutes.
Raising the pH works in the same direction. The more alkaline the water, the harder it is for metals to stay in solution, so a dose of a pH plus product can trigger the discolouration even without shocking. With manganese the threshold is lower still than with iron, which is why manganese often shows up first — and in a darker, purple-black form.
The practical consequence for you is a single one: as soon as you know or suspect that there are metals in the water, shocking is not the first step but the last. Shocking water with untreated iron in it means manufacturing a precipitate that settles on the liner and, on longer contact, writes itself into it as a permanent stain.
The correct procedure when filling from a well
The order of the steps matters more here than the particular products. Anyone who follows it usually never encounters the stains at all.
- Have the water analysed. Before the season, have your well water analysed at an accredited laboratory and ask specifically for iron, manganese, copper, hardness and pH. The analysis costs on the order of tens to just over a hundred euros and it is the only figure you can build on. Home test strips for iron give a rough orientation, but for manganese they are not reliable.
- Remove the metals at the inlet. If the analysis shows elevated values, the best solution is not to let the water into the pool untreated at all — fill through an iron-removal (and manganese-removal) filter, or through a mechanical filter with suitable media connected to the hose. For boreholes with a high iron content this is cheaper than repeated chemical rescue operations.
- Add a sequestrant BEFORE chlorination. A sequestrant, more often labelled a metal stabiliser or a metal remover, binds dissolved metals into a complex in which they no longer react with oxidising agents. Always dose it into freshly filled water and always according to the instructions for the particular product — the dose differs between brands, sometimes by several times. Run the filtration and let the product distribute through the whole volume.
- Only then adjust the pH and shock. Once the sequestrant has been distributed, adjust the pH into the 7.0–7.4 range and carry out the start-up disinfection. In this order the water stays clear.
- Dose the sequestrant on an ongoing basis. Sequestrants gradually break down in pool water, so a single dose does not hold for the whole season. The maintenance dosing — for most products on a scale of weeks — is given in the instructions; the same applies after every larger top-up with well water.
If you use a sequestrant, expect disinfectant consumption to rise slightly. After every such intervention, therefore, check the free chlorine and top it up if needed — how to measure correctly is summarised in How to test pool and hot tub water.
How to remove stains that have already formed
With fresh stains your chances are good; with those that have been sitting on the liner for several seasons, be realistic — some of the discolouration may remain.
Mechanical removal does not work. On a liner or on laminate there is no point in scrubbing the stain. The metal is written into the surface layer of the material, not sitting on it. Abrasive cleaning only dulls the surface, and next time the stain will settle in the damaged spot even faster. Liner care is summarised in How to choose a pool liner.
Products for removing metal stains. The simplest route is a specialised product designed for exactly this purpose. They work on the principle of reduction and chelation — they convert the metal from the wall back into dissolved form. Follow the instructions for the given product exclusively: they differ in the required pH level, in whether the disinfectant needs to be lowered, and in the contact time.
Ascorbic acid. A well-known procedure widespread among pool owners uses ascorbic acid, that is, powdered vitamin C. It works as a reducing agent: it converts oxidised iron back into dissolved form and the stain disappears, over larger areas often within tens of minutes to hours. There are, however, three things you need to know in advance. First, ascorbic acid consumes all the free chlorine in the pool — after the intervention the water is practically without disinfection and it has to be restored. Second, the dissolved metal is still in the water, so a sequestrant has to follow immediately after the treatment, otherwise the stain will return with the first dose of chlorine. Third, for copper stains it is generally not recommended — the reaction may deepen the discolouration instead. This procedure is an intervention into the entire chemistry of the pool, so carry it out according to the instructions for the particular product and with a tester to hand.
Lowering the pH. Most procedures for metal stains work in the lower part of the pH range, because more acidic water keeps metals in solution. Always lower it according to the instructions and gradually, checking the alkalinity — a sharp drop in pH below 7.0 is precisely the state that releases copper from the heat exchanger and sets off corrosion of metal parts.
Partial water change. When the discolouration is extensive and the metal concentration high, the quickest and cheapest route is to drain part of the volume and top up with metal-free water — typically from the mains. Where to put the drained water is dealt with in the article Where to put water from the pool.
Stain colour → likely metal → what to do
| Colour of the stain or water | Likely origin | Typical trigger | First steps |
|---|---|---|---|
| Brown to rusty orange | Iron | Filling from a well, corrosion of pipework | Sequestrant, then a metal stain product or ascorbic acid according to the instructions |
| Brownish purple to black | Manganese | Well water, raised pH | Water analysis, sequestrant, a specialised product for dark coatings |
| Blue-green, turquoise | Copper | pH below 7.0, copper algaecide, heater heat exchanger | Adjust the pH to 7.2–7.4, stop the algaecide, sequestrant; do not use ascorbic acid |
| Greenish grey, water clarity changes | Algae, not metal | Low chlorine, warmth, too little filtration | Brush, adjust the disinfection and the filtration running time |
| Tea brown, but the water is clear | Tannin from leaves and needles | Organic fall | Net and vacuum out the organic matter, only then chemicals |
| Whitish grey coating, rough to the touch | Calcium, not metal | High pH, hard water | Measure pH, alkalinity and hardness, use a scale remover |
| Purple crystals around the jets | Copper + cyanuric acid | Long-term high stabiliser | Measure the CYA, partially dilute the water |
Prevention that genuinely pays off
An analysis of the well water before the season. Once a year, ideally in spring before filling. Besides the metals you will also learn the hardness, which is the second thing that reliably makes pool water unpleasant — the connections are discussed in Water hardness and scale.
Watch the pH because of corrosion. A stable pH in the 7.0–7.4 range is the cheapest protection for metal parts there is. Water with a pH below 7.0 dissolves copper from heat exchangers and attacks steel; water above 7.6 precipitates metals and calcium onto the walls. Regular measurement is the basis, not a luxury — see How to test pool and hot tub water.
Do not combine copper algaecides with a low pH. The worst possible combination: an algaecide containing copper, acidic water and a high chlorine stabiliser on top of that. That is exactly the recipe for blue-green and purple stains. The link with cyanuric acid is explained in Chlorine stabiliser and cyanuric acid.
Top up in smaller doses. When you have to top up from the well, add the water gradually and with the filtration running, rather than several cubic metres at once. A smaller dose of metals is diluted in a large volume and the sequestrant can cope with it. Check the pH and the disinfection immediately after topping up.
Deal with the metal parts too. Rusty marks under the ladder, by the steps or at the cover anchors are not worth tackling with chemicals — there, replacing the corroded part or switching to a stainless steel version is what helps. Spare parts belong to the structural parts category.
When it becomes a question for a professional analysis
Home chemistry has its limits and it is good to know them. Turn to a laboratory analysis, and possibly to a water treatment designer, when the stains come back even after a correctly performed sequestrant treatment, when the water is discoloured immediately after every top-up, when you suspect both iron and manganese in the borehole, or when blue-green discolouration appears in a pool with heating — there it is often a case of ongoing corrosion of the heat exchanger, and what awaits you is equipment servicing rather than chemistry.
Frequently asked questions
The water was clear after filling from the well, and turned brown after the first chlorination. What now?
Stop dosing any more chlorine and do not dose pH plus. Iron has precipitated in the water. Add a sequestrant according to the instructions, let the filtration run continuously and capture the precipitated particles by filtration, if necessary helping things along with a flocculant and vacuuming to waste. Once the water has cleared, adjust the pH and top up the disinfection.
Does a flocculant help against metals?
Against iron that has already precipitated, yes — it joins the fine particles into flocs that can be captured or vacuumed out. Against dissolved metals that have not yet oxidised, no; there a sequestrant is what is called for. Be careful with cartridge filtration, where a flocculant quickly clogs the media.
How long does a dose of sequestrant last?
It depends on the product and on the load on the water; the order of magnitude is weeks. Sequestrants gradually break down under the action of oxidising agents and UV radiation, so they are dosed repeatedly according to the instructions, and additionally always after a larger top-up of water.
Can I use ascorbic acid in a hot tub as well?
A hot tub has a small volume, a high temperature and more sensitive equipment, so the whole intervention is more aggressive and harder to dose. With a hot tub filled from a well it is usually quicker and cheaper to change the water and next time to fill through a filter with suitable media. The rhythm of water changes is covered in How often to change the water in a hot tub.
Will rusty stains disappear on their own if I leave them alone?
They will not. On the contrary, the longer the metal stays on the surface, the more deeply it writes itself into the liner or the laminate and the smaller the chance of complete removal. With fresh stains the success rate approaches one hundred per cent; with stains several seasons old the result tends to be only partial.
Metals are dealt with when filling, not after shocking
The whole problem of rusty stains rests on a single misunderstanding: metals in freshly filled well water are invisible, so nobody allows for them — until the first dose of chlorine makes them visible. Anyone who has the water analysed, fills through a filter and adds a sequestrant before the disinfectant will not need to read this article a second time.
Sequestrants, products for removing metal stains, flocculants and testers for iron and copper can be found in the water treatment category. Further guides to pool care are waiting in the Guide section.
