Pool Algae Series — start here

How to kill pool algae: step-by-step guide

To kill pool algae, raise free chlorine to shock level (CYA × 40%), brush all pool surfaces daily, run the pump continuously, and hold FC at shock level until the water passes the overnight chlorine loss test. Green algae clears in 3–7 days; mustard algae needs an algaecide and gear decontamination; black algae can take 1–2 weeks of sustained treatment.

Identify your algae type first

The core treatment is the same for all algae types — shock-level FC, brushing, and filtration — but the details differ. Misidentifying the type is why treatments often fail.

If your water is green or teal, you have green algae. If you see yellow-brown patches on the walls that brush off and then reappear days later, that's mustard algae. Dark spots that feel rough and don't brush off easily are black algae. See the dedicated guides for mustard vs. green algae and black algae for detailed treatment for each.

Step 1: Test your water before adding anything

You need three numbers to treat algae correctly:

• Free chlorine (FC) — your starting point for calculating how much to add
• CYA — sets your shock target. Without this you're guessing the target. A test strip won't read FC high enough during treatment; use a FAS-DPD drop test.
• pH — if pH is above 7.8, correct it to 7.4–7.6 before shocking. High pH makes chlorine roughly three times less effective.

Step 2: Brush the entire pool

Brush walls, floor, steps, behind ladders, and any other surface before adding any chlorine. Algae forms a protective biofilm layer that shields the cells beneath it from chlorine. Brushing disrupts that layer and exposes the algae to the treatment. This step is non-negotiable — chlorine alone without brushing is significantly less effective.

For green algae: a standard nylon pool brush works. For black algae: use a stainless-steel wire brush on the spots to scratch through the hard protective shell. For mustard algae: brush aggressively toward the drain so dislodged cells get captured by filtration.

Step 3: Raise FC to shock level

The shock target is FC = CYA × 40%. This is the concentration where chlorine destroys algae and breaks down combined chlorine (chloramines) faster than they reform. Below this level, you're adding chlorine that the algae absorbs without being killed.

Use liquid chlorine (sodium hypochlorite, 10–12.5%) to shock. It acts immediately, adds no CYA, and doesn't affect calcium hardness. Do not use trichlor tablets to shock — they dissolve slowly and each ppm of FC raised adds 0.6 ppm CYA, which raises your shock target further and makes the problem worse.

Step 4: Hold shock level and run the pump 24/7

Adding chlorine once isn't enough. Algae consumes FC rapidly, especially during the first 24 hours. Test every 4–6 hours during the day and re-dose whenever FC drops more than 2–3 ppm below the shock target. This is the "hold" part of the process — it's active work, not a one-and-done treatment.

1. Add liquid chlorine at dusk. UV destroys unprotected chlorine fast. Evening dosing gives treatment all night to work before sun exposure.
2. Run the pump continuously. 24/7 during treatment. Circulation brings algae cells in contact with chlorine and keeps dead cells moving toward the filter.
3. Clean the filter every 8–12 hours. Backwash sand or DE filters; rinse cartridge filters. A clogged filter slows clearance significantly.
4. Brush again every morning. Knock freshly killed biofilm into the water column where filtration can remove it.

How to know when the algae is dead

The water looking clear is not enough. Algae can appear gone while still alive at low concentrations that will bloom again within days. All three of these conditions must be met before stopping:

The OCLT is the most important check. Turn the pump off at dusk, record FC, then test FC first thing in the morning before the pump runs. If FC drops more than 1 ppm overnight, there is still active organic demand — algae or organics being oxidized in the dark. Keep going.

Green algae: expected timeline

Green algae (the most common type) follows a predictable color progression during treatment:

• Day 1: Green water begins to lighten or turn cloudy grey. This is normal — dead algae cells are clouding the water before the filter removes them.
• Day 2–3: Water turns milky white. Continue holding FC, brushing, and cleaning the filter frequently.
• Day 3–7: Water clears. Run the OCLT before declaring victory. Light cases may clear faster; heavy blooms with high CYA can take longer.

If the pool goes cloudy during treatment, that's a sign the treatment is working. Don't stop. See dead algae but water still cloudy for what to do in the post-kill phase.

Mustard algae: extra steps required

Mustard algae is a chlorine-resistant strain that will return even after a successful shock if you skip these steps. After brushing and raising FC to shock level:

1. Add a quaternary ammonium or polyquat algaecide per the product label (after shocking, not before).
2. Wash all swimsuits in hot water and dry on high heat — mustard algae spores survive on fabric and reintroduce the problem after the pool clears.
3. Clean all pool toys, floats, brushes, and vacuum heads with a dilute chlorine solution.
4. Clean the filter media thoroughly — backwash or replace as appropriate.

Skipping the decontamination step is why mustard algae "always comes back." The spores reenter the pool on the first swim after treatment. See mustard algae vs. green algae for the complete treatment process.

Black algae: the hardest type

Black algae (technically cyanobacteria) is the most stubborn algae problem in residential pools. It forms a hard protective shell and roots its holdfasts into plaster and concrete. You won't see it in vinyl-liner pools.

Treatment requires a stainless-steel wire brush to physically break the shell before each chlorine dose — otherwise the chlorine sits on top of the protection and never reaches the cells. Expect 1–2 weeks of sustained shock-level FC, daily wire brushing, and possibly a targeted algaecide applied directly to the spots. Full detail in black algae in a pool.

If algae keeps coming back

Recurring algae is almost always a water-chemistry pattern problem, not a one-time event. The most common root causes:

• FC regularly drops below the minimum for your CYA level (target range: CYA × 7.5% for non-salt pools)
• CYA has crept above 60–80 ppm, making chlorine ineffective at normal dosing levels
• The previous treatment was stopped before the OCLT passed — algae survived at low concentration and regrew
• Algae survived on swimsuits or pool equipment between treatments (mustard algae specifically)

Finding the pattern requires tracking readings over time. If you can't see when FC dropped below target or how quickly CYA has been rising, you can't fix what you can't measure. See why algae keeps coming back for a full diagnostic guide.

Related reading

• How to shock a pool — the full step-by-step shock-and-hold process
• FC/CYA chart — your shock target and minimum FC at every CYA level
• Pool turned green overnight — emergency triage for a fresh bloom
• Dead algae but pool still cloudy — what to do after the kill
• Why won't chlorine stay in my pool? — diagnose ongoing FC loss
• Pool shock calculator — exact liquid chlorine dose for your pool and CYA
• Overnight chlorine loss test — pass/fail verdict for your shock treatment