Quick Reference
- What it looks like: yellow, tan, or brown powder on walls and floor. Looks like dirt or sand
- Where: shaded walls, steps, behind ladders, dead spots with poor circulation
- Tell: brushes away in a cloud, comes back to the same spot within a day
- Treatment: SLAM at your CYA-appropriate shock level, held until it passes, plus daily brushing
- You do not need: a specialty "mustard algae" product or a copper algaecide
- Also required: decontaminate everything that touched the water
Table of Contents
What Mustard Algae Is
Mustard algae, also called yellow algae, is a true green algae despite the color. It carries extra pigments that mask the chlorophyll, which is why it shows up tan or yellow-brown instead of green. (You may see it described elsewhere as a bacteria. That is wrong, and the confusion comes from black algae, which genuinely is a cyanobacteria.)
What sets it apart from ordinary green algae is where it lives and how it behaves. It clings to surfaces rather than clouding the water, it favors shade and low-flow corners, and it hangs on at chlorine levels that would wipe out a green bloom.
Identifying It
Mustard algae looks like someone dusted your pool with dirt or fine sand. It sits in patches on walls, steps, and the floor, usually in shade or behind something.
The brush test settles it. Brush the patch. Real dirt lifts and gets filtered out. Mustard algae lifts in a cloud, resettles, and is back in the same spot within 24 hours. That return is the diagnosis.
Rule out the cheap explanations first. Pollen, dead algae from a treatment you already ran, and sand blowing back through a filter with a cracked lateral or standpipe all look similar. Sand coming back through the filter reappears too, so if brushing keeps producing grit near the returns, check the filter before you commit to a week of shocking.
Why It Survives Normal Chlorine
Green algae dies quickly at a properly maintained free chlorine level. Mustard algae does not. It tolerates more, it shelters in low-circulation pockets where chlorine barely reaches, and it recolonizes from whatever survived on a ladder rail or inside a filter.
The practical consequence: a single dose of shock will knock it back and it will return in days. What kills it is holding an elevated chlorine level continuously until it can no longer come back.
Treatment
This is a SLAM, the same process used on a green pool, run with more attention to brushing and gear.
Your shock level depends on your CYA. There is no universal ppm number. Anyone who tells you "shock to 30 ppm" without asking your cyanuric acid level is guessing. Test CYA first, then look up the matching shock level on a Trouble Free Pool FC/CYA chart. At 30 ppm CYA that is roughly 12 ppm FC. At 80 ppm CYA it is far higher. Both are correct for their pool.
The process
- Test everything. CYA especially, since it sets your target. Bring pH to about 7.2 before you start. You will not get a reliable pH reading once FC is very high.
- Clean the filter. Do this first, not last. A dirty filter is a reservoir.
- Raise FC to your CYA-appropriate shock level using liquid chlorine. Liquid is the right tool here. Trichlor and dichlor would drive CYA up mid-treatment, which raises your target as you go.
- Hold it there. Test and re-dose several times a day. Letting FC sag is the single most common reason this fails.
- Brush daily, hard, hitting every shaded surface, step, corner, and light niche. Pull the ladder if you can and brush behind it.
- Run the pump continuously and clean the filter whenever pressure climbs.
- Keep going until it passes all three checks (below). Not until the water looks fine. It will look fine well before it is done.
Knowing when you are finished
All three at once:
- Overnight chlorine loss test: FC at dusk, FC at dawn before sun hits the water. A loss of 1 ppm or less means nothing is consuming chlorine overnight.
- Combined chlorine at or below 0.5 ppm.
- No visible algae anywhere, including behind and under things.
Then let FC drift down naturally to your normal range. Do not swim until it is back within the normal band for your CYA.
Decontaminating Your Gear
This is the step people skip, and it is why mustard algae comes back a month later. It survives on anything that has been in the water.
During the SLAM, put it all in the pool. The shock-level water is your disinfectant. Toss in brushes, poles, vacuum heads, hoses, floats, toys, thermometers, skimmer baskets, and the ladder if it is removable. Swimsuits and towels go through a hot wash.
Anything that cannot go in, including automatic cleaners with electronics, needs cleaning per its manual.
What About Algaecide
You do not need one, and copper-based algaecide is a poor choice here.
Copper stays in your water. It does not break down or get consumed. It stains plaster blue-green, it stains blonde hair, and once it is in there the only way out is dilution. Using it as a recurring maintenance dose, which some treatment plans recommend, means steadily accumulating a staining metal to solve a problem that sustained chlorine already solves.
See our algaecide entry for where algaecides do make sense. Preventing a bloom on a pool you are closing, or covering a stretch where you cannot dose regularly, are legitimate uses. Killing an active mustard bloom is not one of them.
Same goes for products marketed specifically as mustard algae treatments. Read the label. Most are a copper algaecide, a polyquat, or an oxidizer you already own, at a markup.
Keeping It Gone
- Hold FC in the correct range for your CYA, every day. This is the whole game. Nearly every recurrence traces back to chlorine sagging.
- Keep CYA in a sane range so the required FC stays practical.
- Brush shaded areas and steps weekly.
- Fix dead spots. Adjust return eyeballs so the whole pool moves.
- Do not share brushes, poles, or floats with another pool without disinfecting them.
Spas
Mustard algae is uncommon in a properly sanitized spa, and the economics are different anyway. A spa holds a few hundred gallons. Draining, cleaning surfaces, replacing or thoroughly cleaning the filter, and refilling is usually faster and cheaper than running a multi-day SLAM.
If you do treat rather than drain, remember your target still depends on CYA, and dichlor-fed spas often run high CYA without the owner realizing it.