How To Remove Brown Algae From Your Fish Tank

Brown algae (diatoms) can be a real pain. It’s not dangerous, but it looks awful and makes your tank seem dirty and gross.

Diatom blooms are really common in newly set up aquariums. It’s a stage that almost every tank has to go through.

In this guide, you’ll be walked through not only how to remove brown algae, but also how to prevent it from returning in the future.

1. Perform Water Changes to Remove Brown Algae

Doing frequent water changes is one of the best ways to help remove brown algae.

When you do change out water, it removes the nitrates and phosphates that the brown algae eats.

Make sure to really get down in the substrate with a gravel vacuum. Fish waste falls down to the tank floor and sinks into the gravel.

All that waste constantly puts off nitrate and phosphate. Getting it out of the tank helps to starve out the diatoms.

2. How to Remove Brown Algae from Tank Glass

For this, I really like to use a scrubbing pad. Make sure it doesn’t have any added cleansers or soaps. Just the plain cheap kind works the best.


  • Scrubbing pads
  • Small bucket of water


  1. Take the scrubbing pad in your hand and put it against the glass just above the substrate.
  2. Keep steady pressure on the scrubby as you pull your hand straight up until you get above the water line.
  3. Take the scrubby out of the tank and squeeze it out in the bucket.
  4. Repeat this until you have cleaned all the glass in the aquarium.

I know this technique can seem a bit of a pain.

That’s because it is.

But, doing it this way means you wipe off the brown algae and keep it from floating around in the tank.

If you just move the scrubby up and down along the glass, diatoms that you scrub off the glass will go into the water column.

Then they’ll float around and start growing somewhere else in the tank.

Wiping from bottom to top, and wringing out the scrubbing pad, removes more diatoms from the tank.

3. How to Remove Brown Algae from Substrate

Gravel vacuuming aquarium

I’ve split this into two parts for you: Gravel and Sand.

Removing Brown Algae from Gravel

The best way to get brown algae off your gravel is with a gravel vacuum. Really push the lift tube down into the gravel.

As the gravel tumbles around, most of the diatoms should come off and get sucked out through the hose.

Removing Brown Algae from Sand

Not gonna lie, sand is a bit trickier. It easily gets sucked up into the siphon.

  1. Wave the gravel vacuum just above the surface of the sand to get any fish waste.
  2. Then, pinch off the hose so there is very little suction.
  3. Stir up the sand really well with the gravel vacuum to break loose the brown algae.
  4. Pick the gravel vac up out of the sand, unpinch the hose and get up as much of the cloud of algae as you can.
  5. Keep repeating this process until you’ve cleaned up all the sand.

4. How to Remove Brown Algae from Fake Plants and Other Decor

Brown algae build up in aquarium

It’s best to remove fake plants and decor from the tank to get the diatoms off. That way, the ones you scrub off don’t just attach themselves somewhere else in the tank.

You can scrub the algae off with a soft-bristled scrub brush or clean toothbrush.

Sometimes though, you need to pull out the big guns, meaning bleach. Especially for decor with hard to get spots or resin decorations where the paint might come off.

Frankly, I find bleaching much easier for plastic plants that have all the little impossible to clean spots on them.


  • Buckets
  • Bleach (plain bleach with no added scents or other ingredients)
  • Measuring cup
  • Tap water
  • Dechlorinator


  1. Mix 1 part bleach to 20 parts tap water.
  2. Let decor soak for 10 minutes.
  3. Dump the bleach mix and rinse until you can’t smell bleach anymore.
  4. Fill a bucket with fresh tap water and add 5 times the normal tank dose of dechlorinator.
  5. Soak decor for 10 minutes.

5. Improve Lighting

Improving the lighting in your tank can help encourage green algae to grow. It’s actually easier to control the green algae.

So having green algae in the tank instead of brown can make things easier.

Plus, there aren’t very many critters that will eat diatoms, especially in a freshwater tank.

But, there are lots of fish and invertebrates that will happily munch on true algae.

Add lighting that provides a broader spectrum of light and that reaches the bottom of the tank.

Improving lighting can also help live plants thrive. The plants can then out-compete the diatoms for nutrients in the water column.

6. Species That’ll Eat Brown Algae

I’m not ask you to chow down, rather, you can introduce some species into your tank that’ll gobble up your brown algae.

Freshwater Species that Eat Brown Algae

Nerite Snails – these little guys are great at eating up brown algae. They also cannot breed in a freshwater aquarium. So you don’t have to worry that you’ll end up with hundreds of them. They’ll scour any surface in the tank and won’t eat up live plants.

Amano shrimpthese freshwater shrimp will eat brown algae and just about any other kind of algae that grows in a tank. But, they really won’t clean the glass in your tank.

Other Speciesotoclinus catfish and bristlenose plecos may eat brown algae, but they also might not. The nerites are a safer bet.

Saltwater/Marine Species that Eat Brown Algae

Trochus snailsgenus of marine snails with a conical shell. They are great at cleaning up diatoms on all tank surfaces. They’re also a cool species because they can right themselves if they get flipped over, unlike many other snail species.

Mexican Turbo snails (Turbo fluctuosa) – turbos are also very efficient at eating diatoms off of live rock, tank walls and substrate. They are nocturnal and a larger snail that might not be great for small setups.

Find the Root Cause of Your Brown Algae Problems

The most efficient and fastest way to remove brown algae and keep it gone, is to start by identify it’s root cause.

Let’s go through what you should be checking.


Having excess silicates in the tank is just way too tempting for diatoms.

It’s like wearing meat pants in a tiger cage, it’s not gonna go well for you.

When you add new sand substrate, especially play, blasting or pool sand, it creates a huge spike in silicates. Eventually, the diatoms should eat up the silicate and then die off, but this could take months.

Some salt mixes for marine tanks contain silicates. Check the label and consider changing brands if your salt mix contains silica.

High Nitrates

Nitrates are a natural byproduct of the nitrogen cycle. As fish waste breaks down, it puts off ammonia (NH3 ).

The beneficial bacteria in your filters and substrate process the ammonia and create nitrite (NO2 -1). Then the nitrite gets turned into nitrate.

Over time, nitrate can start to build up in your water if it’s not removed by water changes.

Brown algae loves to eat nitrate (true algaes love it, too). It’s like steak dinner with a side of steroids for this stuff.

Test for nitrate levels in your tank. Ideally you want to maintain less than 20 ppm. At all times.

Pro Tip: Keeping nitrate levels low in your tank is the single most important thing you can do to maintain a healthy aquarium. High nitrates help fuel algae outbreaks and can stress fish, making them more prone to disease. Always do weekly water changes.

Make sure to also test your tap water. Some water supplies pick up nitrate from things like agricultural runoff or lawn chemicals. It doesn’t harm humans when they drink it, but it can make things complicated for a fish tank.

High Phosphates

Every aquarium has phosphates. In fact, every living thing depends on phosphate as an essential nutrient, even you.

So phosphate is literally a part of life and there’s no getting away from them completely.

But, if phosphate levels get too high in your tank, they can help fuel both diatom and true algae blooms.

In an aquarium, uneaten food, fish waste, dead plant material, all of it puts off phosphate as it breaks down.

You should test both your tap and tank water to see just how much phosphate is floating around.

Pro Tip: Ideal phosphate levels depend on the kind of tank and the stock you keep.

Freshwater fish only – 0.5-1 ppm
Freshwater planted – 1.5-3 ppm
Reef tanks – 0-0.03 ppm

Poor Lighting

Brown algae thrives in dim lighting that would starve other algae species.

In a tank with bright lights, green algae out-compete brown algae for nutrients in the water column.

9 Ways to Prevent Brown Algae from Coming Back

So you’ve managed to beat the brown algae down.

But how do you make sure it doesn’t come back?

1. Increase Filtration

Increasing filtration can really keep brown algae gone. Diatoms love to eat the organic compounds that come from uneaten food and fish waste as it breaks down.

Make sure that your filter is rated for the size of your tank. This will help process waste more efficiently and help keep the water in the tank moving.

If your current filter is not up to snuff, you can always add on a sponge filter to give you a boost or upgrade to an external canister filter. They’re cheap, easy to set up and run and really add a lot of biofiltration.

2. Keep Up with Your Water Changes

Keeping up with aquarium maintenance is so important to keep brown algae (and other pesky things) from popping back up.

Changing out water gets rid of the nitrates and phosphates that brown algae needs to live. Take away the food, and suddenly your tank doesn’t seem so appealing to the diatoms.

Make sure to do 25%-50% water changes each week.

3. Increase Water Flow

Brown algae really doesn’t like high water flow. It prefers more stagnant water. Increasing water flow means that they can’t anchor onto surfaces and start to grow.

Adding additional powerheads and making sure there are no “dead zones” in the tank can go a long way towards keeping diatoms from coming back.

4. Avoid Silicates

Silicates can hitch a ride into your tank in several ways.

Some water supplies have added silicates in the tap water. See the “Use RO Water” section below for how to deal with this.

Many claim that excess silicates can come from using play sand or other silicate-based sand as your substrate. The theory is that these substrates slowly leach silicate into your water and the diatoms happily set up shop and eat it.

Another source can be using regular table salt in your aquarium.

Some fish, like certain African cichlids and livebearers, need at least some salt in the water all the time.

But, if you use regular table salt as your source, it also has added silicates as an anti-caking agent.

Pro Tip: If you’re going to add salt to your tank, use aquarium salt or pool salt. These do not have the added silicates

5. Avoid Overfeeding

You’ll see lots of sources state that overfeeding causes a lot of problems.

That’s because it’s true!

Overfeeding causes all sorts of problems, including nuisance diatoms and algaes.

You should only feed your fish what they can eat in about 30 seconds (3 minutes for fish who eat really slowly).

Here’s why. Uneaten food sinks to the bottom and puts off tons of nitrate and phosphate. It’s bad news and can really foul your water.

Also, even if your fish eat all the food, if you feed them more than their bodies need, all the extra just gets passed through as waste.

More waste means more nitrates and phosphates. And the more you feed, the more you need to clean the tank.

So don’t overfeed!

6. Use a UV Sterilizer

UV sterilizers pass water through a tube with a very bright UV or UVC light. The light can kill algae, diatoms, bacteria and even some viruses that pass by in the water.

The UV can kill any floating diatoms so they don’t have a chance to attach and grow on surfaces.

Pro Tip: UV sterilizers are a great investment. Not only can they help with algae blooms, but are a great way to prevent disease in your aquarium.

7. Use Reverse Osmosis (RO) Water

Some tap water can have high nitrate, phosphate and added silicate levels. So you might want to consider investing in an RO unit to help cut down on impurities.

These filters push water through membranes that are so fine that it removes almost all other substances. RO water is usually about 95% pure.

Pro Tip: RO units take all of the minerals out of water. All species of fish need at least some calcium and magnesium to replace what their bodies use up. You should add minerals back to RO water with things like Seachem Replenish or Weco Wonder Shells

8. Chemical Filtration

There are several chemical filtration options out there that can help remove silica, nitrate and phosphate from your tank water.

Fresh and Saltwater

Seachem Phosguard – Phosguard is an aluminum oxide (Al2O3) filter media that removes both silicates and phosphates.

Seachem PhosGuard 1 Liter
Seachem PhosGuard 1 Liter

    Last update on 2024-05-23 / Commissions Earned / Images from Amazon Product Advertising API

    Seachem Phosbond – Phosbond combines aluminum oxide and granular ferric oxide (Fe2O3) that removes silicates and phosphates.

    Seachem PhosBond Phosphate Silicate Remover Aquarium Filter Media, 250ml
    Seachem PhosBond Phosphate Silicate Remover Aquarium Filter Media, 250ml

      Last update on 2024-05-23 / Commissions Earned / Images from Amazon Product Advertising API

      Poly-Bio-Marine Poly-Filter – Poly-Filter absorbs nitrate, phosphate and some forms of silica.

      Saltwater Only

      Reactors – reactors pump water into a chamber with chemical filter media that traps phosphates and silicates. Aluminum oxide and granular ferric oxide trap these impurities and help starve out diatoms.

      Two Little Fishies ATLPBR150 GFO PhosBan Reactor 150
      Two Little Fishies ATLPBR150 GFO PhosBan Reactor 150

        Last update on 2024-05-23 / Commissions Earned / Images from Amazon Product Advertising API

        Pro Tip: Activated carbon does not remove nitrate, phosphate or silica. It can remove some dissolved organic compounds, but not the main culprits that fuel diatom and algae outbreaks.

        9. Protein Skimmers

        Sorry freshwater folks, but this section is only for the saltwater aquarists.

        In really simple terms, a protein skimmer pumps extremely fine bubbles through water that creates a foam.

        Things like fish waste and other nutrients stick to the bubbly foam and get forced up to the top of the skimmer where it’s collected. Clean water sinks and passes back out of the skimmer.

        Protein skimmers are great because they remove wastes before they get the chance to break down and put off nitrate and phosphate.

        They can help cut down on excess nutrients that help fuel diatoms, cyanobacteria and nuisance algae.

        Pro Tip: A protein skimmer is highly recommended for any tank over 30 gallons. This will help cut down on the need for large water changes.

        Brown Algae FAQs

        What is Brown Algae (Diatom)?

        Brown algae (class Phaeophyceae) isn’t actually a algae at all. It’s made up of little single-celled organisms called diatoms.

        There are several different species of brown algae (diatoms), some freshwater species and some marine algae.

        They’re one of those little organisms that’s almost always present in any aquatic environment.

        Usually, a few of them hang out in the background and you don’t even notice they’re there. But, sometimes conditions are right for them to pop up in huge numbers, called a diatom bloom.

        Even though they’re not really a species of brown alage, you can still just call them brown algae, lots of people do. In this article I’ll use both terms interchangeably.

        Diatoms get lumped in with true algae because they are very similar. They both need light to grow, they eat organic wastes like nitrates (NO3-) and phosphates (PO4) out of the water column.

        And they can both be a real pain in the butt if they get out of control in your tank.

        What makes brown algae different from true algae is that it also needs silica (SiO2) to live, but algae does not. Silica is a natural compound made up of silicon and oxygen. Diatoms use it to build tough outer cell walls for themselves.

        Brown algae is very common in new tanks. Normally, a few weeks after a tank starts to cycle, diatoms start to appear in the tank.

        Before the nitrogen cycle gets up and running, the nutrient balance in the tank can be out of whack. The diatoms pop up to eat these excess nutrients.

        They usually go away on their own after a few weeks, but sometimes it can take several months.

        But sometimes diatom blooms crop up in established tanks. This is usually a sign that there is some kind of imbalance in the tank that needs to be addressed.

        Can Brown Algae Harm Your Fish?

        Don’t worry. Brown algae won’t hurt your fish at all.

        It just looks yucky.

        How to Identify Brown Algae?

        The easiest way to identify brown algae in a freshwater tank is simply by the color. It’s…well…brown. It’s usually a rusty brown or mustard color. It grows in a thin layer over the glass, substrate and just about any other surface in the tank.

        If you rub a little piece off your glass with your fingertip, it should feel a little bit gritty.

        In marine tanks, there is something called cyanobacteria that can look similar to brown algae.

        The best way to tell diatoms from cyanobacteria is how easily it comes off a surface.

        With diatoms, you have to rub or wipe them off. And only the part you are touching will come off. It doesn’t peel off in sheets.

        Cyanobacteria is different. You can grab a piece and peel it up in big sheets or clumps.

        Pro Tip: Only peel cyanobacteria as an experiment/diagnostic tool. Peeling it up might be tempting, but this will only break off pieces that will colonize other parts of your tank!

        Even just strong water current will usually blow cyanobacteria off.

        Basically, if it comes off really, really easily, it’s cyanobacteria and not diatoms. Also, cyanobacteria will have lots of little bubbles clinging to it all the time. Diatoms do not.

        Katherine Morgan
        Katherine Morgan

        Hey, there! I'm Katherine from Northwest Florida. An aquarium specialist, I've kept tanks for over two decades, enjoy experimenting with low-tech planted setups and an avid South American cichlid enthusiast.


        1. Amazing resource for new aquarists. I’ve learned what type of algae I have (cyanobacteria, not diatoms), how they appeared, and different ways to reduce them in my tank! I also found out other aquarium basics like reactors and protein skimmers, that I always heard people talking about, but never knew their purpose or how they worked. Very well covered topic. Amazing job! Thank you.

        2. Hello,
          I’m Vicky from landlocked Oklahoma. A relatively new aquarist of marine aquariums, I just want to say thanks for this article. It is the best layman’s information based on science I have read or heard. I was told that using sunlight to grow phytoplankton could cause diatoms to be in the plankton. While this article did not address this statement directly, it did address The relationship between lighting, diatoms and green algae. Thanks again.

        3. Great article! Very informative and useful. I particularly liked the part about the meat pants. Thanks!

        4. Excellent information and clear descriptions. The most helpful video I’ve seen covering this topic and so useful for a neophyte freshwater aquarist like myself! Great job!

          • Due to my brown algae bloom I have read loads of articles, but not really understood them.
            This is brilliantly clear and basic for the non expert aqueous owner like myself, Thank You Charlie

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