What Is Brown Algae in Your Aquarium and How to Remove it

Oh brown algae, the nemesis of many hobbyists and professional aquarists alike.

But algae can be found in almost any tank. Usually, it’s not cause for immediate alarm.

It is often a sign of underlying water quality issues, though. And it’s worth getting under control so that it doesn’t get worse.

So we’re going to go over what Brown Algae is and how to remove it!

All About Brown Algae or Diatoms

What is Brown Algae

First things first, “brown algae” and “diatoms” are interchangeable names for the same thing.

The interesting thing about brown algae is that it isn’t an alga at all.

The brown grimy substances sitting in your tank is a colony of bacteria. Fortunately, these little guys are relatively harmless to humans and fish.

Diatoms are a type of algae typically found in newly established salt and freshwater tanks. They commonly exist in recently cycled tanks, due to the excess of nitrates and phosphates in the water.

Once a tank is better established following cycling, the diatoms tend to go away after a few weeks.

Unfortunately, diatoms can stay past their welcome if water quality does not improve over the next couple of weeks.

How to Identify Brown Algae

Diatoms look less like algae, and more like a brown or copper dust sprinkled over all the surfaces of the tank—the glass, the substrate, the decorations, everything really.

If you rub your finger over it, it will quickly come off.

If you gravel vac and wipe the sides off the tank, you will also notice the diatoms come back soon.

Diatoms are often confused with cyanobacteria.

Cyanobacteria can be easily distinguished since it comes off in large clumps. It is also relatively harmless.

What is Brown Algae

Why Does Brown Algae appear

Most algae appear in a tank due to an excess of nutrients.

If your new tank sprung up diatoms, don’t panic.

As we already discussed, they are typically in a life-cycle of a tank and should disappear within the next couple of weeks.

Brown Algae is different from most algae because they need silicate to live, which exists in untreated water.

Under normal circumstances, other algae will keep out diatoms once introduced to the tank.

Can Diatoms Harm Your Fish?

No, diatoms are harmless to fish.

If you have a fish or invertebrate in your tank that is particularly sensitive to water quality issues, such as high nitrates, you’ll need to find the underlying cause for the outbreak. This water quality problem actually could affect the fish.

Otherwise, the main concern for diatoms is that they’re unsightly in an aquarium and can make it hard to view the inside of it.

There is even an upside to having diatoms in your aquarium. They convert the CO2 in your tank into oxygen. High levels of oxygen in tanks lead to healthier fish!

How to Remove Brown Algae

There are many different ways to get rid of Brown Algae.

It’s worth noting that these tactics are the same for both Saltwater and Freshwater aquariums.

1. Remove the water in your tank

Water changes are always good practice.

In any aquarium, I would suggest staying on a regular schedule for water changes and adding extra water changes when water quality issues occur.

Overstocked tanks and certain species of fish will produce more nitrates and might require more significant or more frequent water changes.

Be careful if you do have substantial nitrates in your aquarium not to drain your whole tank.

In the case of an emergency, I would suggest doing a 30% water change at a time not to shock the fish. Typically, a 10-25% water change per week is healthy.

2. Introduce phosphate adsorption resin

Phosphates are introduced into your tank through excess food, dead material, carbon, and tap water. So, make sure not to leave uneaten food in the aquarium.

If your phosphates consistently read high, add some phosphate removing products. Seachem has a product that eliminates both silicates and phosphates.

Be sure to dose appropriately since phosphates are still essential to the aquarium.

Kalkwasser and lime water also helps to reduce phosphates. Use with caution, though – Kalkwasser and lime water will naturally raise your water’s pH.

3. Add an animal that enjoys eating algae

A good cleanup crew is a staple for any aquarium.

Many animals enjoy eating diatoms, but some do a better job than others.

  • For freshwater aquariums, I suggest Nerite snails and Amano shrimp.
  • For saltwater aquariums, I recommend trochus snails and Mexican turbo snails.

It’s amazing how quickly a good cleanup crew can make an algae-ridden aquarium spotless.

The downside is that certain fish will eat algae cleaners, so use caution.

Brown Algae Eaters

4. Monitor the nitrate level

Nitrate tests can be found online and at any pet store.

Nitrate will be found in any fully cycled tank and should stay under 5-10ppm, in an ideal world.

Freshwater aquariums can sometimes tolerate 50ppm, but saltwater aquariums should ideally remain at less than 10ppm.

Certain species will not tolerate nitrates and are more sensitive towards them, such as anemones or corals. Algae blooms are a sign of high nitrates.

Removing Nitrates

  1. One of the best ways to maintain low nitrates is to, once again, do regular water changes.
  2. The addition of a protein skimmer is necessary for individual tanks and will help pull out organic compounds and nitrogenous waste.
  3. The third option for lowering nitrates is to buy nitrate-reducing products, although I would suggest this more for reef tanks that need particularly low nitrates.

Nitrates have other implications other than brown algae blooms and your aquarium should be regularly tested.

Sometimes the fix can be as easy as a more extensive water change or decreasing the amount of food offered to your tank!

5. Clean off the accumulated brown algae

Thankfully, diatoms are easy to clean! Here’s how to remove them from different surfaces in your aquarium.

How to clean Tank Glass

A good scrub usually is all it takes to remove diatoms from the surface of your glass.

I prefer scrubbing tools that have long handles to help reach into the tank, particularly if you have fish that will take a nip at you!

A sponge or algae scraper also works well.

This algae grows back fairly quickly, so if you’re mostly concerned about keeping the viewing part of your tank clean, I prefer a mag float. This is an algae scraper that attaches to a magnet, allowing you to clean the inside of the glass.

I also suggest one with replaceable scrapers since they tend to dull quickly.

How to clean Substrate – Gravel 

Gravel vacuuming is one of the most underrated cleaning procedures in aquariums. I would suggest doing it every time you clean your aquarium.

A gravel vac is generally attached to a siphon, which allows you to control the flow. Therefore, you can remove unwanted buildup in the gravel while not removing the gravel itself.

The gravel vac’s purpose is to remove any waste or algae on the surface of the gravel, as well as underneath.

Move any aquarium decorations and siphon under them as well for a more thorough cleaning.

You should see the diatoms disappear as you gravel vac the tank and should be able to go over areas where the diatoms stuck around.

How to clean Substrate – Sand

Sand is a little trickier to clean with a gravel vac, but not impossible.

Decrease the flow on the gravel vac and vacuum through the sand to remove anything underneath the surface.

Alternatively, look into gravel vacs that have cups or mesh that are designed to keep your substrate from going down the siphon.

How to clean Rocks

Take the rocks out of the tank, first. This way, you won’t reintroduce the algae into the water column as you’re cleaning them.

Start scrubbing. A bristle brush should remove any stubborn spots, but sometimes a sponge works just as well.

Sterilize your cleaning equipment after you’re done with them.

Bleach them in a 10% bleach solution and then stick them in some de-chlorinator. Afterward, thoroughly rinse them.

These steps help prevent reintroducing any algae to the tank.

How to clean Plants or Décor

Take any fake plants or décor out of your tank and scrub.

For more thorough cleaning, let the décor soak for 10 minutes in a 10% bleach solution and put it in a de-chlorinator.

I usually use thiosulfate. This de-chlorinator is instant, and you should no longer be able to smell the bleach.

Rinse them in treated water and reintroduce them to the aquarium.

Cleaning filters

Cleaning filters should be on a regular schedule.

Disposable filters and filter sponges are cleaned or replaced according to directions on the box.

Filter socks can be changed as much as twice a week for large systems.

Protein skimmers require cleaning as often as warranted. (If it looks gross, it probably needs a good wipe!)

Filtration systems should be cleaned on separate days to prevent nitrogen cycling.

Keep in mind, if there isn’t enough bacteria available to convert ammonia to nitrite or nitrite to nitrate, your tank will begin to cycle again.

A detailed schedule for cleaning filter media will assist with algae issues while making sure your bacteria still has a good home!

How do you stop brown algae from returning?

If you were able to isolate the culprit of your brown algae congratulations!

If not, make sure to keep testing your water quality regularly and keep a detailed schedule of tank maintenance and feedings.

Tank maintenance is the best way to prevent most issues found in home aquariums.

How to Prevent Brown Algae – Find the Root Cause

Finding the root cause might involve some trial and error if this is an established tank.

If you have a new tank, it is best to continue regularly checking water quality and thoroughly cleaning the tank for the next couple of weeks.

If the issue remains, try addressing some of these issues.

1. High Nitrates

Almost everyone has run into an issue with high nitrates in their aquarium. Consider these questions if your nitrates fall in the undesirable range (saltwater over 10ppm and freshwater over 50 ppm).

Is your tank overstocked?

An overstocked tank will always have water quality issues.

There are general rules for stocking aquariums, but I find it best to research the individual fish. Some fish produce much higher nitrates than others!

Are you doing enough water changes?

Sometimes life gets in the way of a water change, but this can spell trouble for your aquarium if you don’t do them frequently enough.

Aim to do water changes at least once a week, twice if your tank’s nitrates are out of control.

Make sure not to do more than a 30% water change on time; you can, but only in emergencies, more substantial water changes can be very stressful on a system.

Do you need a protein skimmer?

Protein skimmers are excellent at removing nitrogenous waste from the water.

I prefer in-sump protein skimmers to make sure to clean out your protein skimmer whenever it starts to look dirty. I usually clean mine twice a week in between water changes.

2. Poor Lighting

Typically, high lighting can lead to large amounts of algae growth.

Diatoms do not do as well in high lighting conditions, though. So look into either the settings on your light fixture or look into getting a more substantial light source!

How to Remove Brown Algae

3. Increase Filtration

Increasing your filtration will help remove brown algae and other undesirable algae in your tank.

There are three main types of filtration used in aquariums, mechanical, physical, and biological.


Mechanical filtration helps remove unwanted items from the tank while seeding a biological filter.

  • Examples: filter socks, filter sponges, filter cartridges


Biological filtration uses beneficial bacteria to help your tank cycle and remove nitrogenous waste.

  • Examples: ceramic rings, bio-balls, and live rock


Chemical filtration removes impurities from the water.

4. Increase Water Flow

Powerheads and wavemakers are effective for removing different types of algae.

So, if your brown algae convert to that lovely green algae, the wavemakers should help as well.

Research your wavemakers to find one that best fits the size of your tank.

Also, be careful with individual specimens.

For instance, anemones are known to get caught in wavemakers when moving around in the tank.

Wave Pumps can also be rough on particularly sensitive species such as seahorses, which already have a hard time swimming.

5. Avoid Silicates

Diatoms need silicates to survive.

Silicates often leach off substrate over time.

Thorough rinsing of rocks and substrate before they enter the aquarium can help with accidentally introducing silicates to your aquarium.

If you’re too late, don’t worry; simply keep a proper cleaning schedule. Make sure to deep clean each time, including the substrate and a good scrub on any aquarium rocks.

6. Avoid Overfeeding

Overfeeding can lead to many problems in an aquarium setting.

Especially for new aquarists, finding the right balance of food is hard to maintain. Similar to many household pets, or children for that matter, just because your fish looks hungry does not mean they need to be fed.

If your tank is adequately stocked, investigate what each specific species should be eating.

Some species of fish need to eat two small meals a day, while some only need to eat a couple of times a week. Watch your water quality and adjust accordingly.

Make sure all the food given to your tank is eaten, and make sure to remove any excess food from your aquarium.

7. Use Reverse Osmosis (RO) Water

Reverse Osmosis Water, RO Water, removes trace elements from water and can solve many problems in your home aquarium. It’s good for both freshwater and saltwater aquariums.

Phosphate, nitrates, and silicates are all removed from RO water.

RO water can be made at home using four-step systems, which are available online and at pet stores. Once the water is purified, it can be stored in a reservoir for water changes and top-offs.

The only downside is that the stages need to be replaced regularly

If the upkeep is more than you bargained for, many pet stores sell pre-packaged RO water. Which is easier to manage for smaller aquariums.

8. Chemical Filtration

Chemical filtration is helpful if you know the specific cause of your diatom bloom.

For instance, there are phosphate, silicate, and nitrate removers on the market, which are easy to add to your aquarium.

If you’re unsure why your aquarium is having issues, GFO and carbon are excellent additions to any aquarium.

Make sure to put the GFO or carbon into a phosband reactor to prevent phosphates from being leached into your aquarium, and rinse them thoroughly before adding them to the tank.

9. Protein Skimmers

Protein skimmers come in all shapes and sizes. Make sure to get one that appropriately fits your tank, and suits your needs.

Protein skimmers are bulky and intimidating looking, but they’re straightforward machines.

They simply pull particulates from the aquarium.

Organic compounds are removed by the protein skimmer and overflow into the spill cup, which can get pretty nasty!

Protein skimmers, not only remove unwanted waste and impurities from the water but they also lower the nitrates in your aquarium!

Protein skimmers are typically recommended for saltwater aquariums, but can be used in freshwater aquariums as well, especially if there is an issue with nitrate buildup in the water quality!

What to do if none of this works? 

A frustrating aspect of working with live animals in closed systems is that the effects are not always as quick as we would like!

Sometimes it takes months to see the results we want.

I tend to be on the impatient side myself and find it best to take a picture every couple of days to see if things are getting better or worse.

This is a good trick not only for algae blooms but fish health as well.

There are multiple suggestions here, so I would suggest taking them one at a time once the water quality issue is detected.

If you can isolate the problem causing the algae, it might be easier to decide which method(s) you would like to approach to attack your algal bloom!

If you’re looking for a quick fix, you could always use vodka dosing, hydrogen peroxide, or other quick remedies found at the pet store.

The issue with these methods is that certain fish or invert species do not respond well to these treatments.

They also do not address the actual water quality issues at hand and will have to be repeated frequently.

Prevent Brown Algae


I regularly maintain my tank, why do I get diatoms?

Diatoms appear in new tanks, because of an excess of nutrients.

Algae usually mean than an excess of nutrients is available in your tank.

Often when algae exist in an aquarium, something is amuck in your water quality and it might require additional types of filtration or an adjustment on feeding.

General tank maintenance, such as cleaning, gravel vac, water changes, etc. will help prevent many problems.

However, since tanks are not natural environments for aquarium plants and animals, additional care is often needed.

If green algae follow diatoms, why would I want to get rid of diatoms?

Green algae are generally easier to manage.

Generally, fixing the water quality will help keep it under control. Thorough cleanings of tanks will help as well and robust algae eating crew.

Algae is something to pay attention to in your aquarium, but also not something that should make you want to pull your hair out.

Final Word

So now you should have the knowledge that you need to battle diatoms. They’re easy to get rid of with a little patience and the right tools!

If these tips seem overwhelming, start by exploring water quality.

Often when there are issues with your fish or with the appearance of your tank, water quality is the culprit! 

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