How to Identify and Treat Mustard Algae in Your Pool

You’re finally getting some sun, the grill’s warming up, and the pool’s crystal clear. 

Or so you thought.

Then you spot it. 

Some weird yellow gunk hanging out on the pool wall or clustered at the bottom. You brush it off. It comes right back. You brush harder. It laughs in your face.

We hate to break it to you, but that stubborn yellow stuff? It’s likely mustard algae and one of the most annoying pool problems out there.

But don’t worry! It’s not permanent, and you’re not doomed to spend your summer scrubbing pool walls.

We’re going to show you how to kick it to the curb (and keep it from coming back).

What Is Mustard Algae?

Great question! Because this stuff is sneaky.

Mustard algae (aka yellow algae) is a chlorine-resistant, clingy, dust-like form of algae that loves to lurk in shady corners of your pool. Unlike the fluffy green stuff that floats around and turns your water cloudy, mustard algae is more like fine yellow dust that sticks to walls, floors, pool gear, and even your swimsuits.

And yeah, it’s tough. It can survive normal chlorine levels, fly under the radar, and comeback if you don’t hit it with the right stuff. Basically, it’s the pool version of glitter. You think it’s gone, and then boom, it’s back.

So, if mustard algae keeps showing up in the same spots no matter how many times you scrub, you’re not without hope! There are methods to cleaning and preventing it from coming back.

How to Identify Mustard Algae in Your Pool

Mustard algae is a trickster. It doesn’t turn your whole pool green, and it doesn’t float around like regular algae.

Here’s what to look for:

• Dusty yellow or mustard-colored patches on pool walls or floor (especially in the shady spots)
• Streaks or smudges that brush off easily but always come back
• Clingy buildup that hides in cracks, corners, steps, ladders, and under pool toys or floats
• No major water cloudiness — the water might still look clear, which is why this stuff often flies under the radar

Still not sure if there is mustard algae in the pool? Here’s a simple test:

Take your pool brush and scrub a suspicious yellow spot. If it comes off easily but returns within a day or two, that’s likely mustard algae.

Quick Tip: If you notice some yellow buildup starting to form in your pool, don’t wait. Early action is your best friend. Keep your brush handy, and make sure your test strips are up to date. 

Need supplies? Check out our pool care tools and treatments.

How to Treat Mustard Algae in the Pool

Alright, so you’ve confirmed the yellow gunk is mustard algae in the pool. 

The good news? You can beat it. The not-so-fun part? It takes more than just a quick brush and a splash of chlorine. Mustard algae is stubborn, but if you follow this step-by-step plan, you’ll be back to cannonballs and poolside chillin’ in no time.

Step 1: Remove and Clean Everything

Toys, floats, swimsuits...if it’s been in the pool, it needs to be cleaned. Wash soft items in hot water and scrub gear with a diluted bleach solution. Let everything dry thoroughly in the sun before bringing it back.

Step 2: Brush the Whole Pool

Use a stiff-bristle brush to scrub walls, floors, steps, and shady corners. Even spots that look clean might be hiding algae.

Step 3: Vacuum and Clean Your Filter

Vacuuming right after brushing helps remove all the algae you just loosened up.

If your system has a “waste” setting on the filter valve, use it! This sends the dirty water straight out of the pool instead of running it through your filter. That way, you’re not risking mustard algae spores cycling back in. 

No waste setting? No problem! Just vacuum carefully and follow up with a thorough filter cleaning.

After vacuuming, clean or backwash your filter to eliminate anything that snuck through. A clean filter is key to stopping algae from making a comeback.

Step 4: Balance the Water

Check your pH (7.4–7.6), alkalinity (80–120 ppm), and sanitizer levels. Balanced water helps your shock work effectively.

Step 5: Shock It Hard

This isn’t your weekly maintenance shock. You’ll need 3–5x the normal amount. Add it in the evening, then run your pump and filter for 24–48 hours straight.

Need a shock that actually works on mustard algae? Shop our most powerful pool shock here.

Step 6: Brush Again

After shocking, brush all surfaces once more to loosen anything leftover and help your filter catch the rest.

Step 7: Clean the Filter Again

Give your filter another round of cleaning to clear out any final algae debris. Once that’s done, your pool should be looking bright, clean, and back in business. 

Ready to make sure it stays that way? Let’s move on to prevention.

How to Prevent Mustard Algae from Coming Back

You’ve done the hard work. The yellow patches are gone, your water’s sparkling, and your pool is back in business. Now, let’s keep it that way.

Mustard algae is sneaky. It hides in tiny places and waits for your guard to drop. But with a few simple habits, you can stop it from making a comeback.

Keep Your Chlorine in Check

Mustard algae thrives when sanitizer levels drop. Test your chlorine regularly (at least 2–3 times a week) and adjust as needed, especially during hot weather or after heavy pool use.

Brush Weekly

Even if your pool looks clean, brushing helps disrupt anything trying to take hold on your walls, steps, or floor. Make it a regular part of your routine.

Vacuum Regularly

Algae loves to hang out in quiet corners and settle at the bottom. A quick vacuum once or twice a week keeps your pool clean and circulation flowing.

Wash Swim Gear and Toys

Suits, floats, goggles. if it’s been in natural water (like lakes or oceans), rinse it well before tossing it into your pool. Algae spores can hitch a ride and sneak back in.

Shock Occasionally — Even Without Algae

Routine shock treatments help keep your sanitizer levels high and your water clear. A light shock every couple of weeks during peak season goes a long way in prevention.

Deep Clean Monthly

Once a month, take a little extra time to backwash or clean your filter, scrub trouble spots, and double-check your water balance. This helps catch problems before they start.

Prevention doesn’t have to be complicated; it just has to be consistent. A little routine care now means fewer algae battles (and more splash time) later.

Don’t Let a Little Algae Ruin Pool Season

Mustard algae might be a pain, but once you know how to spot it, treat it, and stay ahead of it, it stops being a mystery and starts being just another box on your pool care checklist.

A few simple habits (plus the right gear) are all it takes to stop mustard algae in its tracks and keep your pool sparkling from the first cannonball to the last sunset swim.

Shop Pool Supplies Now and keep your water clear, clean, and algae-free all season long.