Black Algae in a Pool: Why It Keeps Coming Back (and How to Actually Kill It)

Black algae is the one that makes people feel like they’re losing. You brush it, you shock the pool, and a few days later the same dark spots are back in the same places. Here’s why: it isn’t algae, there’s no bottle that kills it, and the fix is mostly elbow grease. Once you understand what you’re actually fighting, the method makes sense.

What black algae actually is

Despite the name, black algae is cyanobacteria — a bacterium, not a true algae. Three things make it the hardest thing to get out of a pool:

• It hides under a waxy cap. Cyanobacteria build a tough protective layer (Orenda calls it a chlorine-resistant peptidoglycan/biofilm layer) that chlorinated water beads off of instead of soaking into. Your chlorine gets used up on the outside before it ever reaches the living cells.
• It cements itself into the surface — and no, it has no roots. A 2025 peer-reviewed study that sequenced black algae from 15 pools found mostly one genus, Leptolyngbya, anchoring itself with extracellular polysaccharides and hair-like pili — glue, not roots. A Florida lab that put it under a microscope calls the “roots” people describe EPS projections. The glue locks it into the pores and micro-cracks of plaster, gunite, and concrete, which is why it’s rare in smooth vinyl and fiberglass pools. The practical result is the same as a root would be: it’s dug in where a brush and a splash of chlorine can’t reach — so the treatment is mechanical either way.
• It’s built for the fight — and it moves. The industry’s own water-quality committee (PHTA, writing in AQUA in August 2026) spells out why it shrugs off what kills green algae: its pigments — phycocyanin and carotenoids on top of chlorophyll — protect it from sunlight and oxidizers and let it grow in shade; some species pull nitrogen straight out of the air; and the filamentous kinds glide slowly across the surface on their own slime, creeping out of cracks and shaded corners into low-flow areas. That last one matters for treatment: a fragment you brush loose can settle and reattach somewhere else if your chlorine isn’t already high enough to kill it in transit.

And the root cause is almost always the same: chronic under-chlorination. Free chlorine spent too long below the minimum for your CYA, and a spore that blew in on the wind or rain got its opening. Trouble Free Pool notes black algae is more common in the South and South Florida — where warm water keeps it active year-round (more on that below).

First, make sure it’s actually black algae

Three things get mistaken for it. Confirm before you spend two weeks treating the wrong thing:

• The fingernail-smudge test (the tell): scrape a spot with your fingernail and smudge the sample on plain white paper. A greenish streak means black algae.
• Dark aggregate, not algae: worn white plaster and pebble finishes can show dark stone underneath, especially near steps. It won’t smudge greenish and it won’t grow.
• A metal stain, not algae: rust-colored marks (often from iron fertilizer granules that blew in) are stains — they lighten under a crushed vitamin-C tablet. See pool stains, scale & scum to tell marks apart.

The behavioral tell: black algae regrows in the same spots after brushing. A stain doesn’t. It also isn’t green algae (free-floating, clouds the water, brushes away easily — see my pool is green) or mustard algae (yellow, dusty, wipes off but comes back). Black algae is dark, raised, firmly attached, and stubborn.

The method that actually works

There is no shortcut and no magic bottle. The job is: break the cap, hit it with concentrated chlorine, hold free chlorine high for weeks, and brush daily.

1. Break every spot open

You have to physically disrupt the waxy cap so chlorine can reach the cells underneath:

• A few spots (under ~10): a bamboo skewer or a wood stick to dig each one out works.
• Many spots: a weak pressure washer with the widest tip (like 45°), held about 18 inches off the surface — carefully, because a pressure washer can damage plaster. Start wide and far, move closer only if needed.

A stiff stainless brush can break the surface too, but some experienced owners consider a wire brush too aggressive for plaster — and it will shred a vinyl liner (though black algae is rare on vinyl anyway). The cap reforms quickly, so scraping the top layer once isn’t enough — you’ll be breaking it open again and again over the treatment.

2. Spot-dose with strong liquid chlorine, then hold it high for weeks

Right after you break the spots open, hit them with the strongest liquid chlorine you can find (usually 12.5%) — pour it down the wall over the spots, or spray it on with a pump sprayer. On white plaster only, the direct-contact alternative PHTA describes is rubbing a trichlor tablet or a pinch of granular chlorine straight onto each broken spot — maximum dose exactly where the cells are. Not on colored plaster (it bleaches), never on vinyl or fiberglass, gloves on, and keep it to a handful of spots: trichlor is acidic and carries CYA. Then hold the whole pool high: Trouble Free Pool’s black-algae number is free chlorine at about 20% of your CYA, held for 2–4 weeks (their example: CYA 70 → keep FC near 14 ppm), never letting it drop. That is half a full SLAM, held far longer — and if the pool is also green or cloudy, run the SLAM first and then settle into the 20% hold. Find your rows here (the SLAM figure is the ceiling you never need to exceed for black algae alone):

• Target FC band (read it off the chart)
• Minimum FC (≈ 7.5% of CYA)
• Below minimum — algae can grow

If you do need the full SLAM, walk through it in my pool is green — the process is the same; black algae just adds the cap-breaking and a much longer hold afterwards.

3. Brush the spots daily

This is the part that decides whether you win. Because the cap reforms, brushing the affected spots every day is what keeps re-exposing the cells to your elevated chlorine. Skip days and the colony re-shields itself and survives. And brush with the chlorine already at the hold, never before it gets there: PHTA’s point about gliding is that the fragments a brush frees can drift, settle and reattach in a new spot unless the water kills them on the way. Keep free chlorine at the 20% hold and brush daily until the spots are gone and stay gone — then drop to weekly brushing, and keep inspecting the hiding places (behind lights, under steps, around ladders, inside the skimmer). Trouble Free Pool is blunt about the aftermath: once a pool has had black algae it is more susceptible, and the floor becomes 12–15% of CYA, never lower, for the life of the plaster.

On plaster or gunite only. Stainless bristles will destroy a vinyl liner and can scratch fiberglass or paint — and black algae is rare on those surfaces anyway. A small detail head beats a full-width wire brush here: you want your force concentrated on the spot, not spread across the wall.

If your pool is vinyl or fiberglass

Everything above hands you a tool you can’t use, so here’s the version for a liner.

First, doubt the diagnosis. Black algae anchors into the pores and micro-cracks of plaster and gunite. A vinyl liner and a fiberglass shell are smooth and non-porous, so there’s very little for it to dig into — which is why it’s genuinely rare on these surfaces (PHTA’s one caveat: where water barely moves, even a smooth surface isn’t immune, so a liner’s dead corners are where to look). Re-run the smudge test before you treat anything: scrape the spot with a fingernail and rub it on white paper. No greenish streak means it isn’t black algae, and on a liner the usual answers are a stain, or ordinary algae sitting in a wrinkle, a step seam, or behind a light niche where circulation dies. A dark patch that won’t smudge, won’t lighten, and doesn’t change at all with brushing may be growth behind the liner — no brush and no chlorine level reaches that, and it’s a liner question rather than a chemistry one.

If it really is black algae, the mechanical step changes and the chemistry does the extra work.

• No wire brush, and no pressure washer. The guide above warns a pressure washer can damage plaster — a vinyl liner is far softer than plaster, and you also risk stressing seams and pulling the liner in its track. Don’t point one at a liner.
• Break the caps by hand instead. A bamboo skewer, a wood stick, or a plastic scraper on each individual spot does the job without touching the surface around it — the same tool the guide recommends for a handful of spots on plaster, and on a liner it’s the whole method rather than the small-job option.
• Then lean on the chlorine side. Because you can’t be as aggressive mechanically, the cap gets broken less thoroughly each pass — so the part that compensates is holding the 20%-of-CYA chlorine level for longer and brushing the spots more often, not harder. Nylon is the bristle type that’s safe on a liner at all; that’s the one to use, every day, until the spots stop coming back.

For that daily brushing — and for every other pool on earth — you want nylon, which is safe on plaster, vinyl and fiberglass alike. One caution that’s specific to liners: the brush below is built to multiply the force you put into the wall, and GABco itself says to use care around corners, steps and the wall-to-floor transition — which is exactly where a liner is easiest to damage, and exactly where growth on a liner usually turns out to be hiding. Ease off in those spots and let the chlorine do that part of the work.

The stuff that wastes your money

• “Black algae treatment” bottles don’t do the mechanical work — they can’t break the cap or reach into the plaster pores. The brush does that. In fairness, PHTA’s committee does write that “regular treatment with an algaecide specific for black algae can prevent reoccurrence” — note the word is prevent, not kill; EPA doesn’t review an algaecide’s efficacy claims; and holding chlorine at ratio is the prevention that’s free and proven. We don’t recommend one.
• Copper algaecide is actively harmful. It adds copper that permanently stains your surfaces and turns blond hair green, and it doesn’t leave the water. Don’t.
• Silver algaecide (“Silver Algaedyn”) is the same trap with a better label. The label says “completely effective against black algae” — but EPA does not review efficacy data for algaecides, so that is the maker’s word. The only controlled test on real pool black algae used silver at 100–300 times a pool dose, in a lab dish, and its authors propose it as a grout coating for prevention. In chlorinated water most of the silver you pour in precipitates as silver chloride, which sunlight turns into black metallic silver on your plaster — the label’s own small print admits it “can sometimes stain pools”, and no home test kit can tell you how much silver is in the water. Trouble Free Pool and Orenda both say no metal algaecides, full stop.
• Phosphate remover is not part of the kill. The makers say so themselves — Orenda: “simply removing phosphates does not kill (or starve) algae.” Two reasons it is actively unhelpful on a black algae job: the phosphate test reads wrong while there is still biomass in the pool (the algae is holding the phosphate), and lanthanum phosphate can clog a cartridge or DE filter during the weeks you most need circulation. Hold your chlorine and it is irrelevant; Trouble Free Pool documents pools that stay clear above 4,000 ppb. PHTA adds the biology: cyanobacteria store phosphate inside the cell and some species fix nitrogen from the air, which is why its committee concludes that nutrient limitation alone “is not an effective strategy” against black algae.
• Enzymes can soften the protective layer (Orenda notes this), but you still have to brush — nothing replaces the mechanical step.
• The one honest exception: Polyquat 60 is a legitimate winterizing preventative, not a cure. It won’t dissolve an established colony.

If a store hands you a “black algae kit,” you’re paying for bottles to do a job a brush and liquid chlorine do better. That’s the whole pool-store playbook.

Keep it from coming back

• Hold free chlorine at 12–15% of your CYA every day, forever — chronic under-chlorination is the root cause, and Trouble Free Pool’s post-black-algae floor is that ratio for the life of the plaster (CYA 50 → never below 6–7.5 ppm). See the 5 numbers for the chart.
• Look at WHERE it grew. The spa footwell, the steps, tight corners, bench joints, behind the ladder — black algae establishes first where water barely moves. Be clear about the causality, because Trouble Free Pool’s moderators are: algae shows up first in the dead spots, but “the cause is always the poor FC/CYA, not the poor circulation.” Fix both (PHTA: where flow is low, even smooth surfaces aren’t immune). Brush those spots weekly on purpose, and if a step or spa has no return near it, pool-service companies’ standard move is to angle the nearest return eyeball down and across the mouth of that pocket (or run the pump longer) so chlorinated water actually reaches it — practical, not a cited method. Badly pitted plaster may need resurfacing to win for good.
• Expect it late in the season, and don’t count on winter. Outbreaks cluster in late summer and early fall when the water is warmest (PHTA), and a colony a cold snap seems to have killed has usually just gone dormant in the pores — PHTA is explicit that it “will not simply die off in the winter months” but waits for the water to warm. Keep brushing the old spots into fall and hold your ratio through the shoulder months.
• Kill the introduction routes: disinfect a brush or net that’s been in another pool, wash swimsuits and toys that have been in a lake or pond first, and rinse feet before jumping in — moist soil tracked in from the yard is on PHTA’s list of ways it arrives, alongside wind, rain runoff, fill water, animals and even insects. (The CDC warns against ever filling a pool straight from a lake, river, or pond.)

The Florida angle

Warm water keeps cyanobacteria active year-round. A northern winter doesn’t kill the colony either — PHTA says it goes dormant in the pores and waits — but it does stop the growing months; Florida pools don’t even get that pause, which is exactly why Trouble Free Pool notes black algae is more common in the South and South Florida. Two practical consequences: hold your chlorine at ratio all twelve months (no coasting), and pay attention to the shaded, low-flow corners under a screen enclosure — the cage’s shade and calmer water in the corners create the dim, still micro-spots black algae likes. (This is environmental reasoning, not a Florida-specific study — but it’s why FL pools see more of it.)

Bottom line: black algae isn’t a chemistry failure you fix with a better bottle — it’s a bacterium dug into your plaster under a chlorine-proof cap. Break the cap, hold free chlorine at about 20% of CYA for weeks, and brush the spots every single day. Skip the “black algae” products entirely, never reach for copper, and once it’s gone, keep your chlorine at the CYA ratio year-round so it never gets the opening again.