How To Get Rid of Brown Algae in Your Fish Tank

How To Get Rid of Brown Algae in Your Fish Tank

If you’ve experienced a brown algae breakout in your tank, you’ll know what a horror it can be.

By rapidly coating the aquarium glass and your gravel, rocks, and plants, brown algae is exceptionally unattractive and ruins your tank’s look.

It can also be bad for your freshwater plants or your corals in a saltwater tank.

We’re going to see what brown algae is, how to get rid of brown algae in your fish tank, and also how to prevent it from occurring.

What Is Brown Algae?

First things first, although almost everyone calls brown algae “brown algae,” really it’s not algae at all!

Algae is a kind of plant, but what aquarists commonly call brown algae is something called a “diatom.” 

A diatom, or “brown algae,” is actually a tiny animal and not, in fact, a plant at all! 

However, in terms of keeping a fish tank, these patches of thousands of connected tiny diatoms act and look pretty much like regular green algae in all except their color, so brown algae is a reasonable term to use for us non-scientists. 

Brown algae can grow on the tank glass, spread across gravel substrate and rocks, cover plant leaves, and in a saltwater tank crust over corals.

All in all, whatever we call it, it’s definitely not something we want in our tanks!

How To Identify Brown Algae

You’ll know brown algae in your fish tank by the brown, sometimes film like patches that appear on your glass, the substrate, decorations, and on plants.  

It might start as a semi-transparent brown film and then get thicker.

Typically brown algae is slimy to the touch.

Generally, the patches of diatoms are only loosely attached to the surface, and so it can be wafted or gently wiped away quite quickly.

What Causes Brown Algae in a Tank?

The diatoms that are brown algae are naturally occurring.

They’re just generally in such small quantities that we don’t see them.

What isn’t natural is them being so numerous that they join together in colonies and spread across the fish tank to make brown algae patches.

Brown algae outbreaks are generally caused by an imbalance of certain nutrients in the aquarium’s water. This can be silicates, nitrates, phosphate, or a combination of all three.

Silicates, Nitrates, and Phosphates

High levels of silicates, nitrates, or phosphates in your tank water will cause brown algae to grow.

We need to understand where these nutrients can come from to be able to balance them in our tank and control the brown algae.

In general, the source can be a combination of more than one factor.

While some of these can be connected to not following general good aquarium husbandry, some might be more complicated and not necessarily obvious initially.

Where Can Silicates Come From?

Silicates come from two primary sources:

  • Your water supply
  • Gravel substrate or rocks

Where Can Nitrates Come From?

Nitrates are likely to come from:

  • Your water supply
  • Aquarium plant fertilizers
  • Decaying fish food from overfeeding
  • Decaying plant material
  • Fish waste buildup

Where Can Phosphates Come From?

Phosphates can come from:

  • Your water supply
  • Aquarium plant fertilizers
  • Decaying fish food from overfeeding
  • Decaying plant material
  • Fish waste buildup

All of these factors, alone or combined, can cause brown algae to grow uncontrollably.

You might have noticed that there are some common causes for all three of the nutrients, so when we look at how to prevent brown algae, we will start by looking at these.

Brown Algae in New Tanks

It is quite normal to get a small amount of brown algae in a new fish tank while it is cycling.

Usually brown algae in a new tank will appear in the first week or so and then disappear after a few days once the tank has settled.

So long as you don’t overload the new tank with fish too quickly, then a little bit of brown algae, in the beginning, isn’t anything to be overly concerned about and will probably go of its own accord.

Step-by-Step Guide for Removing Brown Algae

So you’ve got a bad case of brown algae? No worries! Let’s take a look at how we can remove it and leave your fish tank lovely and clean once again!

We’ll assume that the algae problem is a bad one and take you through step by step cleaning the tank from top to bottom.

Before you start, make sure that you wash your hands well and remove jewelry and watches.

Rocks and Decorations

The best way to clean rocks and other decorations is to remove them from the aquarium carefully.

Detritus can also gather underneath tank decorations, so removing them allows you to clean up thoroughly.

Once the decorations are out, you can give them a good clean with a soft brush to remove the algae.

Rinse them well with fresh water before returning to the tank after you’ve finished the cleaning.

For really dirty or hard to clean decorations, take a look at our FAQs where we’ll talk about giving them a deep clean.

Plants and Corals

The leaves of plants can be wiped gently in situ with a soft sponge to remove the algae.

For small plants wafting your hand over them gently in the water can usually shift the algae from their leaves.

For corals, again, gentle wafting your hand over the coral usually is sufficient. If not, a small syringe or turkey baster can be useful to use a directed blast of water to push the algae away.

The dislodged algae can then be removed by the tank filter or siphoned out in step 4.


Just wipe it down with a soft sponge.

Any dislodged algae can then be removed by the tank filter or siphoned out when you clean the substrate.

Pro Tip: Aquarium filter floss works remarkably well and is excellent at trapping the algae as you clean the glass so that it can be removed entirely from the tank and discarded.


Having carried out all the above steps, the dislodged brown algae will either be being collected by your filter or settling on the substrate.

Let it settle and then use an aquarium gravel cleaner to suck it all up and maybe do a partial water change at the same time along with a filter clean.

Ways To Prevent Brown Algae From Coming Back

Having got rid of the brown algae, you’ll want to make sure that it doesn’t come back.

Good general aquarium husbandry techniques can make a significant contribution to stopping your algae problem.

It might be necessary also to do some investigation to find out the root cause and stop it from making your tank an algae disaster again.

Water Testing

If you get an outbreak of brown algae with no apparent cause, then you need to test your water.

Test your tank water, but also test the freshwater you’re using for filling the tank and for water changes.

You can buy simple test kits for silicates, nitrates, and phosphates to check the nutrient levels.

High levels of silicates, nitrates, or phosphates in the tank could be solved by doing a larger than routine water change, but in the long term, they could also be caused by some underlying reasons that we’ll look at in a moment.

However, if the tap water you’re using for water changes is already high in nutrients, it might be necessary to get a water filter to solve your problem.

A water filter can remove high nutrient levels and make the water suitable for filling the tank and water changes. 

RO Filters are commonly used to clean the water for saltwater tanks where the nutrient levels are critical to control.

Water Changes

Many algae outbreaks are caused by aquarists not carrying out regular water changes on their tanks.

Every aquarium needs small, regular, partial water changes to dilute waste products that build up even in the best aquarium.

You should change about 20% of your tank’s water each week.

This can be an excellent opportunity to give the tank a clean up inside and then siphon off the waste to leave everything clean while removing the water.

Remember that the replacement water must be the same temperature as the tank and that you need to use an aquarium water conditioner and let the water settle before adding it back.

You can also use a UV sterilizer to help reduce the occurrence of algae and bacteria.

Aquarium Filtration

Ensure that your filter is adequate for the aquarium’s size and the number of fish you have.

If you’re experiencing lots of brown algae outbreaks, you might need to upgrade your filter system, or it might be that you need to clean it more frequently.

Remember that waste material trapped in a mechanical filter needs to be cleaned out periodically. 

Clogged filters will pollute the tank with nitrate and phosphate and feed the algae.

If you’ve tested your water and found high levels of nutrients in the tank that can’t be consistently reduced with partial water changes, then you can look at adding special filter media that can reduce the levels of silicate and phosphate, and nitrates.

Water Movement

Make sure that your aquarium has adequate water movement throughout the tank.

Waste materials that should be collected by the filter can accumulate in dead water spaces.

You can help reduce dead water spaces by adding an extra pump or air diffuser into the aquarium.


Overfeeding is a widespread reason for algae to bloom.

Waste food creates an excess of nutrients in the water that overwhelms your filter.

Ensure that you only give as much food as your fish will eat in a minute or so, and always remove any uneaten food with a net or gravel cleaner.

Substrate and Rocks

Silicate can come from gravel substrates or natural rocks used to decorate your tank.

Make sure that you only buy rocks and substrates that are sold as “aquarium safe.”

Regular sand used in play pits, for example, can contain high levels of silicate.

If you’re unsure, place some of the rock or sand in some clean water that you’ve already checked, and then after leaving it for a few days, re-test levels of silicate, nitrate, and phosphate and see if they’ve gone up.

If they have, then the substrate or rock is the likely cause and shouldn’t be used in your tank.

Algae Eating Tank Mates

Luckily, you can add some fish and other critters to your tank that will eat the brown algae.

It’s best to sort out the underlying cause that’s making the brown algae grow, but adding in a few of the following can help keep the tank generally clean. 

Just make sure not to overload the aquarium and create more problems!

For Freshwater:

  • Nerite Snails 
  • Amano shrimp
  • Otoclinus catfish
  • Bristlenose plecos 

For Saltwater:

  • Trochus snails 
  • Turbo snails

Frequently Asked Questions About Brown Algae

Is Brown Algae in an Aquarium Good or Bad?

The negative effects of brown algae in the tank are reasonably obvious.u003cbru003eu003cbru003eThe patches are ugly, can prevent us from seeing through the tank glass clearly, cover our decorations and substrates, and generally are not what we want to see!u003cbru003eu003cbru003eMore importantly, perhaps, brown algae can smother our plants’ leaves and prevent them from receiving sufficient light and causing them to die.u003cbru003eu003cbru003eIn a saltwater tank, the algae can smother corals leading them to suffer or die also.u003cbru003eSo from this point of view, we definitely don’t want extensive brown algae growths.u003cbru003eu003cbru003eThere is an argument that brown algae will consume carbon dioxide in the tank and release beneficial oxygen.u003cbru003eu003cbru003eTruthfully this small benefit is far outweighed by the visual problems and health negatives that brown algae can cause.

How Do I Get Brown Algae off My Fish Tank Decorations?

The easiest way to remove brown algae from your decorations is to carefully remove them from the tank and give them a good clean.u003cbru003eu003cbru003eYou want to take all decorations out slowly to take as much of the algae with the piece as possible. You don’t want the brown algae falling off and being left in the tank where it will be harder to remove.u003cbru003eu003cbru003eWhether it’s plastic plants, rocks, or any other decoration, the process for cleaning is basically the same.u003cbru003eu003cbru003eGive the piece a good wash under flowing fresh tap water. You can scrub the algae off with a soft brush such as a toothbrush or cleaning brush for larger pieces.u003cbru003eu003cbru003eTo stop any small missed pieces of algae from growing back, you can soak the decorations in a mild chlorine bleach solution. This will kill off any areas of algae that you might have missed scrubbing.u003cbru003eu003cbru003eMix 1 part bleach to 20 parts tap water in a bucket and leave the decorations to soak for ten minutes.u003cbru003eu003cbru003eYou should then rinse the items under freshwater until you can’t smell the chlorine bleach anymore.u003cbru003eu003cbru003eSoak the decorations for ten minutes in another bucket of fresh water with an aquarium dechlorinator conditioner dosed for the bucket’s volume 5 times its normal strength to make sure all chlorine from the bleach is gone.u003cbru003eu003cbru003eRinse the decorations one final time and return them to the fish tank, good as new.

Do You Leave Fish in the Tank When Cleaning?

Yes, you can leave the fish in the tank while cleaning.u003cbru003eu003cbru003eUnless you’re doing a really huge cleaning job, it’s generally less stressful for the fish if you leave them inside the tank.u003cbru003eu003cbru003eOnly consider moving them to a holding tank if you’re doing a full strip-down and clean.u003cbru003eu003cbru003eTry not to leave it so long that the brown algae is so bad you have to rip everything apart to clean up!

Do LED Aquarium Lights Cause Brown Algae?

There’s no evidence LED lights cause brown algae in a fish tank. In fact, proper lighting can help reduce brown algae as it enables your plants to grow, which will allow them to remove the nitrate and phosphate nutrients that brown algae can otherwise use as food.

Will Vinegar Kill Brown Algae in Fish Tank?

No, vinegar cannot be used to kill brown algae in your tank.u003cbru003eu003cbru003eIntroducing vinegar to your tank will lower the pH of the water, making it more acidic.u003cbru003eu003cbru003eWhile this could potentially affect the brown algae, it will definitely harm your fish and plants and could kill them!u003cbru003eu003cbru003eVinegar is not a good solution to a brown algae problem.

Can Baking Soda Get Rid of Brown Algae, and Is It Safe for Fish Tanks? 

Adding baking soda to your fish tank will raise the pH of the water.u003cbru003eu003cbru003eThe pH value is generally not related to brown algae’s growth, and using baking soda shouldn’t be considered a good treatment for this problem.u003cbru003eu003cbru003eAdjusting the tank’s pH with baking soda should only be done cautiously and in conjunction with carefully testing both pH and KH (Carbonate Hardness) values.

Final Thoughts

Brown algae is an ugly nuisance in your fish tank and can cause harm to plants and corals.

Keeping a generally healthy aquarium with good filtration and making regular water changes with clean water will significantly help.

Remember to test your tank frequently and act on any changes before they get out of hand.

If you do get an outbreak of brown algae, investigate the potential sources that we’ve discussed so that you can find the cause and eliminate it fast.

Looking for tips about aquarium maintenance? Head over to our Aquarium Maintenance & Repair section to see more.

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