Pool algae: green, yellow, black, three species, three different treatments
Green algae responds to standard shocking. Yellow/mustard algae needs 3× the shock and specific brushing. Black algae needs metal brush and weeks of recovery. Treat the right species or you’ll spend a month chasing it.
Last updated: 2 June 2026
Algae is the most common pool problem, but it’s also the most commonly mistreated. Most pool owners assume algae is algae, add shock, brush, wait. That works for green algae (the most common species, ~85% of residential bloom cases). It barely touches yellow/mustard algae, and it does almost nothing for black algae.
The right treatment depends on identifying which species you have. This guide walks through the three common pool algae species, how to identify each, and the specific treatment that works for each.
Identifying the species
| Species | Colour | Where it grows | Chlorine resistance |
|---|---|---|---|
| Green algae | Light green to dark green, suspended in water | Throughout the water column, surfaces in shade | Low, standard shock works |
| Yellow/mustard algae | Yellowish-brown, dust-like | Shaded areas, corners, behind ladders, under steps | High, needs 3× shock concentration |
| Black algae | Dark green-black or black | Plaster pools mostly. Anchored to surfaces, forms raised patches | Very high, chlorine alone barely touches it |
Identify before treating. The wrong treatment for the wrong species wastes chemicals, time, and water, and the algae often gets worse during the failed treatment cycle.
Green algae, the standard case
Green algae is the species that almost every “my pool’s gone green” thread is about. It blooms when free chlorine drops below the CYA-adjusted minimum for more than ~24 hours. It’s suspended in the water column and creates the classic “swamp pool” look.
Treatment
- Test first: FC, pH, CYA, CC.
- Fix pH to 7.2. Lower pH so the chlorine works at maximum strength. Use muriatic acid as needed.
- Brush all surfaces. Walls, floor, steps, corners. This dislodges the biofilm and exposes algae cells directly to chlorine.
- Calculate shock dose. Target FC = max(10 × CC, 40% of CYA). For a 50,000 L pool with CYA 60 and CC 1, that’s ~24 ppm FC, requiring about 9 L of liquid chlorine.
- Add chlorine over 30 minutes through return jets, pump running.
- Hold FC at shock level until water clears AND CC drops below 0.5 ppm overnight AND no further chlorine demand is visible. Typically 2–4 days.
- Filter 24/7 during the recovery. Backwash or clean filter daily.
The 80% rule for green: if FC drops more than 4 ppm overnight during shock, you still have live algae. Re-shock immediately. Once the loss is <2 ppm overnight, the algae is dead and the pool is in recovery filtration.
Yellow/mustard algae, the resistant one
Yellow algae (also called mustard algae) is a different species, Mycaceae chrysophyta. It’s much more chlorine-resistant than green algae and tends to colonise shaded surfaces rather than suspending in water. Common in Australian pools in the warmer northern states and indoor pools with low UV.
Identification
Looks like fine yellow-brown dust settled on horizontal surfaces, corners of the deep end, behind ladders, under stairs, in the shadow of skimmers. It can be brushed up easily but settles back within hours. Distinct from pollen or storm debris because brushing redistributes it without it clearing.
Treatment
- Standard shock won’t work. Yellow algae has 3× the chlorine resistance of green algae. The shock target is 1.5× the normal CYA-based shock, so for CYA 50 ppm, target FC is 30+ ppm (not 20).
- Brush every 2 hours during the active treatment, yellow algae forms a chlorine-resistant biofilm that needs to be physically disrupted continuously.
- Treat pool toys, ladders, brushes, vacuum heads, yellow algae spreads via contamination. Soak any pool equipment in a bleach solution before re-introducing.
- Specific yellow algae treatment products work, Sodium bromide-based treatments are the most effective. Australian brands include HTH Yellow Treatment, BioGuard Banish, and Lo-Chlor Yellow Algae Killer.
- Hold elevated FC for 5–7 days minimum, not the 2–4 days for green algae.
- Backwash filter daily, yellow algae loads filters fast and persists in them.
Yellow algae returns easily. Even after a successful treatment, expect a re-bloom within 6 months if any equipment wasn’t sanitised. Always replace pool brushes after a yellow algae treatment, the brush head harbours spores.
Black algae, the worst case
Black algae is the most resistant species, actually a cyanobacterium, not a true algae. It’s primarily a problem in plaster and concrete pools (rare in vinyl liner or fibreglass). It forms raised, anchored patches that look like dark green or black spots.
Identification
Raised, slimy patches firmly attached to plaster, often in areas with rough texture. Range from 1cm to 10cm in diameter. Brushing exposes a chlorine-resistant outer skin and a pink/grey core. The patches return within days if not properly killed.
Treatment
- Mechanical removal is essential. Standard pool brushes don’t work, use a stainless steel pool brush to physically remove the patches.
- Apply chlorine directly to the patches with a chlorine puck rubbed into the affected area, OR by dropping cal-hypo granular directly on the patches with the pump off.
- Standard shock at 2× the green algae rate, target FC is 80% of CYA, not 40%.
- Hold elevated FC for 7–14 days. Black algae has thick cell walls and deep root structures into plaster.
- Repeat the brushing every 12 hours for the first 5 days, then daily for the next 9 days.
- Algaecide with copper, copper-based algaecides are effective against black algae and approved for residential use. Australian: HTH Black Spot Algaecide, BioGuard Algicide 90.
Severe black algae often requires partial draining and acid washing of plaster. If after 14 days of treatment the patches still return, the algae has rooted into the plaster pores. The fix is draining, acid-washing the affected areas, and replastering or applying a sealant.
Preventing the next algae bloom
Treating algae is reactive and expensive. Prevention is straightforward:
- Maintain FC above the CYA-adjusted minimum daily. The most common cause of bloom is FC sliding below the threshold for 24+ hours.
- Test CYA monthly. If CYA climbs above 80, your FC target needs to climb proportionally, most blooms in “well-maintained” pools are because the owner didn’t adjust FC target when CYA crept up.
- Brush the pool weekly. Even normal-looking pools benefit, disrupts biofilm before it establishes.
- Shock after pool parties or heavy rain, as a precaution. Don’t wait until algae appears.
- Algaecide as preventive maintenance, once per month at maintenance dose is fine. Use a polyquat-based product (copper-free) for routine maintenance, save copper-based products for active treatment.
- Run the pump 8+ hours per day in summer. Stagnant water is algae’s ideal condition.
Algaecide products, what works, what doesn’t
| Product type | Effective against | Notes |
|---|---|---|
| Polyquat (polyhexamethylene biguanide) | Green algae prevention | Best routine preventive. Won’t stain. |
| Copper sulfate | Black algae, severe green | Can stain plaster. Don’t use with chlorine for first 24 hours. |
| Sodium bromide | Yellow/mustard algae | Specific to yellow algae. Effective. |
| Silver-based algaecides | Marketed as broad | Largely ineffective. Mostly marketing. |
| “Mineral cartridges” in skimmer | Marketed as preventive | Marginal effect. Not a substitute for chlorine. |
Most algaecide problems come from over-reliance on algaecide as a substitute for proper chlorination. Algaecide is a supplement to chlorine, not a replacement.
Sources & references
- Trouble Free Pool, ABCs of Pool Water Chemistry
- Richard Falk, The Chlorine/CYA Relationship
- ANSI/APSP-11, Water Quality Standards in Public Pools
- AS 3633-1989, Private swimming pools (Australian Standard)
Frequently asked questions
Why does my pool keep getting algae?
Almost always because free chlorine has been below the CYA-adjusted minimum for more than 24 hours at some point. If your CYA is 80 ppm, your minimum FC is 6 ppm, not ‘1–3 ppm’ as test kit charts say. Most chronic algae problems are CYA problems disguised as chlorine problems.
Can I swim in a pool with algae?
No. Algae itself isn’t directly dangerous, but its presence means your sanitiser level is inadequate, which means bacteria are also present. Wait until water is clear, free chlorine is in safe range for your CYA, and combined chlorine is below 0.5 ppm.
What’s the difference between green and mustard algae?
Green algae is suspended in the water column, light to dark green, susceptible to standard chlorine shocking. Mustard/yellow algae is yellow-brown, settles in shaded corners, and is 3× more chlorine-resistant, needs higher shock concentration and specific brush treatment.
How long does it take to clear an algae pool?
2–4 days for green algae caught early, 5–7 days for severe green or yellow algae, 7–14 days for black algae. The recovery requires continuous pump operation, daily filter cleaning, and holding FC at shock level until the algae is fully killed.
Will algaecide alone clear my pool?
No. Algaecide kills algae more slowly than chlorine and isn’t designed for active blooms. Use chlorine shock for the kill, and algaecide as a supplement after the pool is clear. Algaecide as preventive maintenance is fine; algaecide as a substitute for chlorine is the wrong tool.
Does the Water Test Calculator app help with algae?
Yes. The app diagnoses early algae blooms from FC, CC, and CYA readings before they become visible, then walks through the correct shock dose and recovery timeline. Launching on iOS and Android in approximately 10 days.
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