Guide
How to get rid of mustard algae in a pool
Updated October 8, 2026
Written by Richard Ellis, Certified Pool Operator
Short answer
Mustard algae is a yellow or yellow green film that clings to shady walls and brushes off easily, then comes right back. Kill it by brushing, holding chlorine high for a day or more, and cleaning everything that touched the water, because it hides on swimsuits, toys and pool tools and reseeds the pool.
Mustard algae is sneaky rather than tough. It looks like dirt or sand on the shady side of the pool, it brushes away in a cloud, and two days later it is back in exactly the same place. The trick to beating it is less about the chemical and more about catching the places it hides.
What is mustard algae?
Mustard algae, also called yellow algae, is a chlorine resistant algae that grows as a yellow, yellow green or brownish film on walls and floors, usually on the shady side of the pool. It feels slimy rather than rough, and unlike black algae it does not root into the plaster. It just keeps coming back.
Is it mustard algae or pollen?
Pollen floats, mustard algae sticks. Every spring in Palm Beach County, oak and pine pollen covers pools in a yellow dust. Pollen sits on the surface, collects at the waterline and in the skimmer, and wipes away. Mustard algae clings to the walls and floor, usually in the shade, and returns in the same spots after you brush it off.
If you brush a yellow patch and it is back in the same place two days later, it is algae.
What causes mustard algae in a pool?
Low chlorine, shade and poor circulation let it grow, and gear carries it in. Swimsuits, floats, toys and even pool brushes used in another pool, a lake or the ocean bring it along. Once it is in, it hides in the filter, on the tools and on anything that sat in the water.
What kills mustard algae in a pool?
Chlorine held high for days kills it, but only if you clean everything it can hide on and brush first. The order matters, because the reason it comes back is almost always something that did not get treated.
- Treat the gear. Wash swimsuits, and put toys, floats, brushes and the skimmer net in the pool during the shock.
- Brush the walls and floor to stir it up into the water where the chlorine can reach it.
- Lower the pH to about 7.2 and shock heavily after dark. Hold the chlorine high for at least a day.
- Run the filter nonstop and clean it once the dead algae has been caught, because the filter is a favorite hiding place.
As always, the CDC rule applies: chemicals go in one at a time, never mixed.
Can you swim with mustard algae in the pool?
Not during treatment, and ideally not until it is gone. The chlorine will be far above swimming level, and algae in the water means the chlorine is losing. Wait until free chlorine is back to 5 ppm or lower. See how long after shocking can you swim.
How long does it take to kill mustard algae?
Usually a few days of treatment. Check the shady walls a week later. If it comes back in the same spots, something reseeded it, usually the filter or a piece of gear that missed the shock. If the whole pool has gone green by then, a green pool cleanup is the faster way back.
How do I keep mustard algae from coming back?
Keep chlorine steady, brush the shady walls every week, and keep gear clean.
- Steady chlorine of at least 1 ppm, or 2 ppm with stabilizer, per the CDC.
- Brush the walls and steps weekly, the shady side first.
- Rinse floats and toys used anywhere else before they go in.
- Keep the filter clean. See how often to clean a pool filter.
Brushing the walls and steps is part of every weekly pool service visit.
How to kill mustard algae
- 1
Collect the gear
Wash swimsuits. Put toys, floats, the brush and the net into the pool so they get the shock too.
- 2
Brush everything
Brush the walls, steps and floor, shady side first, to lift the algae into the water.
- 3
Lower the pH
Bring the pH down to about 7.2 so the shock works at full strength.
- 4
Shock after dark and hold it
Add a heavy dose of shock in the evening and keep chlorine high for at least 24 hours.
- 5
Vacuum and clean the filter
Vacuum the dead algae, to waste if you can, then clean the filter thoroughly.
- 6
Check the shady walls in a week
If yellow returns in the same spots, repeat and look for what reseeded it.
Quick answers
- Can you vacuum mustard algae?
- Yes, after it is killed. Vacuum slowly, to waste if your filter allows it, so the dead algae does not go back through the filter.
- Can you get mustard algae in a salt water pool?
- Yes. Salt pools are chlorine pools, and mustard algae grows anywhere the chlorine dips or the water does not circulate well.
- Why does mustard algae keep coming back?
- Something reseeded it: the filter, a brush, a float or a swimsuit that did not get treated. Clean every piece of gear during the shock.
Sources
Keep reading
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