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. Two 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 anchors into the surface. It digs into the pores and micro-cracks of plaster, gunite, and concrete — which is why it’s rare in smooth vinyl and fiberglass pools. People say it “grows roots into the plaster”; technically it anchors with a biofilm rather than true roots, but the practical result is the same: it’s dug in where a brush and a dose of chlorine can’t easily reach.

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 SLAM

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. Then run the full SLAM process: raise free chlorine to SLAM level for your CYA and hold it there for weeks, not days. Compute your number:

• Target FC band (≈ 11–12% of CYA)
• Minimum FC (≈ 7.5% of CYA)
• Below minimum — algae can grow

Walk through the full SLAM steps in my pool is green — the process is the same; black algae just adds the cap-breaking and the longer hold.

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. Keep free chlorine at SLAM level and brush daily until the spots are gone and stay gone.

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.
• 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.
• 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 in range for your CYA every day — chronic under-chlorination is the root cause. If you’ve had black algae, run FC toward the high end of its range (see the 5 numbers).
• Brush weekly so nothing gets a foothold, and fix the dead spots — poor circulation corners and rough, pitted plaster are its habitat. Badly pitted plaster may need resurfacing to win for good.
• Kill the introduction routes: disinfect a brush that’s been in another pool, and wash swimsuits and toys that have been in a lake or pond first. (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, so Florida pools don’t get the winter break a northern pool does — 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 SLAM level 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.