Brown Algae In Fish Tank – 4 Reasons Why (And 9 Ways To Get Rid Of It)

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Brown algae is a common problem in aquariums and one that can leave aquarists frustrated and worried. This type of algae shows up as a brown layer over just about any type of surface. But is bad for your tank? and what can you do to remove it?

In this article, we’ll go in-depth to learn everything you need to know about brown algae in fish tanks and how to keep it under control.

So let’s get started!

Key Takeaways

  • Brown algae (diatoms) are common in new aquariums and usually disappear on their own
  • If brown algae is a long-term problem, its cause can be managed
  • Brown algae is a common aquarium pest that thrives on high silicates, phosphates, and nitrates
  • Increasing regular tank maintenance is a good way to combat brown algae in many cases

What Is It?

Brown algae- also known as silicate algae or diatoms1, are single-celled algae found in fresh and saltwater all over the planet. These tiny algae use light to grow (photosynthesize) and silicate to form a protective ‘glass’ shell. Diatoms are not true brown algae, although they evolved from the same ancestor.

Aquarists think of diatoms as a pest, but these algae are actually vital for life on earth. Like plants, they are the foundation of the food chain, which supports all living animals. These incredible life forms also provide the oxygen we breathe. In fact, diatoms in the ocean are said to produce more oxygen than all the world’s rainforests!

So how do you identify brown algae? These algae settle on pretty much all tank surfaces, including rocks, glass, and substrate. They form a thin, rusty brown layer that is soft and easy to remove.

Is It Bad?

Diatoms are generally not bad for your aquarium. They often show up in new tanks after a few weeks or months and then disappear on their own. However, a slimy brown layer is not very attractive, so in that sense, they are bad.

Despite the ‘dirty’ look, diatoms are a great food source for many aquatic animals, including algae-eating fish. Unfortunately, there are some situations where serious brown algae growth can have real negative effects on your aquarium.

When Are Diatoms Bad?

Sometimes diatoms do not disappear on their own, and they can be a concern in planted aquariums. Brown algae harm plants by covering their leaves and blocking their access to light.

When plants are unhealthy, their leaves begin to decay. Decaying leaves break down and release even more phosphates and nitrates into the water, potentially making the problem even worse.

Let’s take a look at some of the main causes of brown algae in aquariums

Causes Of Diatoms

Understanding the cause of any problem in your aquarium is the first step toward finding a solution. So, it’s time for a little detective work! This information is also useful to prevent brown algae in any other aquariums you put together.

Freshwater Diatoms

1. New Aquariums

The most common cause of diatom growth is a water chemistry imbalance in a newly set-up aquarium. This problem usually happens in immature tanks without healthy populations of beneficial bacteria and other microorganisms.

A covering of brown slime is a big surprise to many new fish keepers, and it’s easy to panic and start looking for complicated and expensive solutions. Rest assured, after a few weeks, other forms of algae will probably outcompete these diatoms, and you may never see them again.

However, if the brown algae in fish tank water do not disappear on their own, or if you develop this problem in a mature aquarium, you may need to look for other causes.

2. High Nitrates, Phosphates, and Silicates

These three compounds are the usual cause of persistent brown algae problems in established aquariums. Let’s take a closer look at each one and how they encourage brown algae growth.

  • Nitrates

Nitrates are the final product of the nitrogen cycle in an established aquarium. They can also be found in low concentrations in tap water and other water sources. Diatoms thrive in high nitrate environments because they use this compound as an energy source for growth.

The best way to limit nitrate is to physically remove it from your aquarium by changing the water. However, you can also manage this nitrogen compound by limiting the amount of fish you keep or by growing aquatic plants.

  • Phosphates

Diatoms and other algae thrive in water with high phosphate. These phosphorous compounds are another product of aquarium waste, like uneaten food and dead plant material.

A lack of maintenance and overfeeding flake foods are major causes of high phosphate levels in aquarium water.

  • Silicates

Brown algae (AKA silica algae) thrive in the aquarium water with high silicate levels because they use silicates to grow a protective shell.

Silicates are salts formed by combining silicon and oxygen. They can come from water sources like tap water and hardscape materials like sand, gravel, and rocks. Silicate concentrations in tap water may vary depending on where you live.

3. Stagnant Water

Brown algae attach themselves very weakly or simply settle on surfaces in your aquarium. Stagnant water with no movement allows them to multiply, while flowing water keeps them suspended in the water column where they can be filtered.

Aquariums should have healthy water flow to keep small waste particles suspended in the water column where your filter can collect them.

4. Poor Water Quality

Diatoms and aquarium algae tend to thrive in low water quality with high nutrient levels. Most nutrients come into your aquarium as fish food and never really leave the system.

Sure, the fish eat the food, but they cannot absorb all of the nutrients, and whatever remains stays behind in the form of fish poop.

Good quality filtration and beneficial bacteria turn these excess nutrients from highly toxic substances into mildly toxic substances known as nitrate. The most efficient way of removing nitrates is through regular partial water changes and growing live aquarium plants.


So now you know a little more about what diatoms are and what causes them, but how do you know which cause applies to your situation? The simple answer is by testing.

A standard aquarium test kit measuring ammonia, nitrite, and nitrates is a ‘must-have’ for any fish tank. A silicate test kit is recommended for an older tank with a persistent brown algae problem.

When To Test

An important thing to remember about testing is that water parameters change over time. Testing once a year or once a month will not give you an accurate idea of what’s really going on with your water chemistry.

Test your water every three days or so in a new aquarium to monitor changes in your water chemistry. You can reduce the frequency to once a week as things stabilize, but I recommend testing before and after water changes to work out a schedule with the right results.

Once your aquarium is established and stable, you can slow down and test once a month or whenever you notice any potential problems like sick fish, algae growth, or unhealthy plants.

How to Get Rid of Brown Algae in Fish Tank – 9 Best Ways

Now that you know a little more about the causes of brown algae problems, let’s go ahead and learn how to get rid of brown algae in your aquarium. We have a video from our YouTube channel that you can also follow along.

1. Give It Time

Brown algae are usually a temporary problem, and the best course of action in many cases is to just watch and wait. The diatoms will clear up on their own in time as other algae establish themselves and the nitrogen cycle develops and matures in your tank.

2. Clean It Up

If your brown algae problem is not solving itself, or you really can’t stand the sight of it, you can always clean it off manually.

Diatoms do not attach themselves firmly like some other algae species, so they are pretty easy to remove. Here’s how:

Cleaning Aquarium Glass

Let’s face it; no one likes dirty aquarium glass. Removing brown algae from tank walls is easy with an algae scraper or a non-scratch algae pad. Use a plastic scraper or a purpose-made algae pad to avoid scratches if you have an acrylic aquarium.

Whatever you use to clean your aquarium glass, take care to never get sand or gravel between the glass and the cleaner because that’s how scratches happen.

Cleaning Aquarium Ornaments

You can carefully remove aquarium ornaments and clean them in old tank water, ideally when doing a water change. This is not necessary if your brown algae problem has just started in a new tank.

Cleaning Aquarium Substrate

Brown algae often settles on the bottom of fish tanks, and this can be pretty unsightly, especially if you have a light-colored substrate. These diatoms can be removed by suction with your gravel vacuum.

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Cleaning Aquarium Plants

Cleaning brown algae on aquatic plants is difficult without damaging their leaves. This job is best left to the experts- the algae eaters!

Keep reading to learn more about aquarium algae eaters later in this article or check out my in-depth guide to the best algae eaters for freshwater tanks.

Cleaning Fake Plants

Many aquarium owners prefer to use fake plants to create a more natural appearance, although cleaning them can be a challenge. You can scrub your plastic plants with a soft brush or cloth or dip them in a mild bleach solution (1/10 parts) or hydrogen peroxide.

3. Change Your Substrate

Brown algae require silicates to grow, but where do they get this material? While it is possible to reduce your silicate levels through filtration, sometimes you need to go straight to the source. Silicates can come in through your water, but they are also found in most substrates. Play sand, for example, is high in silicates.

4. Increase Water Flow

Increasing the water flow in your aquarium can prevent diatoms from settling. You can do this by installing a larger filter or a powerhead. In some cases, just rearranging your hardscape or moving your filter will have a big effect on water circulation.

Of course, some fish don’t do well in strong water flow so this might not be an option with slow-swimming fish like bettas and fancy goldfish.

5. Improve Water Quality

Poor water quality is the cause of so many problems in the aquarium hobby that it’s usually the first place to start when anything goes wrong. But how do you improve water quality?


All aquariums need adequate filtration to support the nitrogen cycle and remove waste particles from the water. There are many types of aquarium filters on the market, but it’s always a good idea to buy the best quality unit that you can afford.

Designs like canister filters that provide more space for filter media can support larger beneficial bacteria colonies and ensure better filtration. Still, you can also use more than one filter in your aquarium as long as you do not create too much flow.

Aquarium filters are usually rated by the tank size they can be used for, but manufacturers often overestimate this figure.

Therefore, the filter’s gallon-per-hour rating is far more useful. As a general guideline, choose a filter that can process the total amount of water in your tank 4 to 6 times every hour.

Adding a protein skimmer to your saltwater aquarium can improve the filtration by removing even more phosphates from the water.


The number one cause of poor water quality is a lack of aquarium maintenance. We all dream of an aquarium that takes care of itself, but the truth is that the water quality in our tanks changes in time, and the smaller the tank, the faster this happens.

Excess nutrients cause water quality issues, and the two most effective ways of reducing these nutrients are to limit the amount that goes in and to remove as much as possible.

If you have too many fish in your aquarium, you’ll need to feed them a lot, and they will produce a lot of waste. Consider stocking your tank with fewer fish if you want to minimize your maintenance needs.

Water Changes

Even with a low-stocking rate, nitrate levels will slowly climb, leading to algae outbreaks and many other issues. Performing more water changes is the simple solution to reducing these excess nutrients.

But how often should you perform water changes? And how much water should you change each time?

Nitrates and phosphates build up at different speeds in different tanks, so the only way to answer these questions is to test your water regularly. Nitrate levels of 20 ppm or lower are considered ideal for fish, although you can usually let them rise to double that without problems.

Put simply, if your aquarium water has a nitrate reading of 30 ppm, a 50 percent water change will bring it down to about 15 ppm. If it takes two weeks to return to 30 ppm, then a 50% water change every two weeks may be necessary.

6. Grow Plants

Healthy plants will compete with brown and green algae to suppress their growth. Live plants use light and nutrients to grow, just like brown algae, and we can all agree that aquarium plants look much better than diatoms!

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However, growing healthy, vigorous plants is not as simple as throwing them into your tank and hoping for the best. Different aquarium plants have different needs, so while some plants will grow like weeds without any care, others will need experience, time, and some extra equipment to flourish.

Here’s what you need to know about plant care:

  • Aquatic plants need light to grow

Use purpose-made aquarium lights to provide the right spectrum of light for your plants, and run your lights on a timer for 6 – 8 hours each day to simulate a natural photoperiod (day/night cycle).

  • Plants need nutrients

You’re probably wondering how adding nutrients could be beneficial when your goal is to reduce nutrients. Well, plants will use nutrients in the water from excess food and fish poop, but they also need other nutrients from fertilizers to perform at their best.

Remember, healthy growing plants will use up the nutrients in the water column before the brown algae, and basically beat them at their own game.

  • Plants need Carbon Dioxide

Did you know that plants breathe in carbon dioxide (CO2) and breath out oxygen? Fortunately, CO2 occurs naturally in our aquarium water column. But some plants need increased levels to thrive.

If your goal is to simply get rid of algae, choose plants that do not need injected CO2 to thrive. If you want a jaw-dropping aquascape full of colorful plants, however, you will want to invest in some extra equipment.

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  • Plants attach themselves in different ways

Aquarium plants fall into three categories; the fastest and easiest are the floating plants. Species like hornwort will float in the water column, soaking up nutrients and competing with diatoms and other algae types like blue-green algae.

Epiphytes do not float or drift but rather anchor themselves to solid structures like rocks and driftwood. These plants use their roots to hold on and to capture nutrients from the water column. Epiphytes will compete with brown algae, although they tend to be slower growers than floating plants.

Rosette plants and rooted stem plants send their roots down into the soil, sand, or gravel to anchor themselves and collect nutrients. Some rooted plants need quality aquarium soil to thrive.

7. Add Animals That Eat Them

Growing live plants is an excellent way to combat many algae species in the aquarium, but there’s another way to use aquatic life to your benefit. One of the easiest (and most fun) ways to control brown algae is to add algae eaters!

Various fish and snail species eat brown algae, and these creatures can be fascinating to keep. While these animals will remove brown algae, they cannot solve the cause of the problem.

Let’s quickly look at some great species that can help you eliminate brown algae.

  • Otocinclus catfish

The otocinclus catfish is a small freshwater fish with a big appetite for algae and diatoms. These fish grow to just 2 inches, and they can be kept in tanks as small as 10 gallons.

  • Amano shrimp

Amano shrimp are another excellent option for diatom control in a freshwater aquarium. These interesting inverts are perfect for planted tanks, but beware, larger fish will eat them.

  • Nerite snails

Nerite snails are hard-working creatures that love to eat diatoms. There are a few different species available, and most have awesome shell patterns or shapes.

Some aquarium snails tend to breed out of control, but not the mighty nerite. These snails cannot breed in freshwater.

  • Plecostomus

Plecos are armored catfish from South America that love to snack on brown algae. There are many species of plecostomus catfish, ranging from the strange bristle nose pleco at 4 to 5 inches to the common pleco that can reach 20 inches. Naturally, choosing the right species for your tank size is pretty important!

  • Lawnmower blenny

So far we’ve only focused on freshwater species that eat brown algae, but there are many great options for marine aquariums too!

The lawnmower blenny is a great little reef fish that grows to just a few inches and is suitable for reef tanks of 30 gallons or more. These expertly camouflaged bottom dwellers may take up to 3,000 bites each day, so they’re great for removing brown algae.

  • Trochus snails

Trochus snails are another excellent option for marine tanks. These conical gastropods come in many patterns and colors, and the various species range from 1 to more than 3 inches across. Trochus snails are easy to care for, easy to breed, and they eat diatoms and blue-green algae.

8. Try Phosphate Removers

It is possible to control diatoms by reducing the amount of silicates in the water. Products like Phos-Zorb from API and Phosguard from Seachem remove both silicates and phosphates from the water to suppress brown algae growth.

9. Use Reverse Osmosis Water

If your tap or well water is very high in silicates, your best option might be to use reverse osmosis (RO) water or RODI water in your aquarium. Reverse osmosis water is pure water that has all contaminants and minerals removed through a filtration process.

However, it is important to note that RODI water for freshwater fish is completely pure and unsafe for fish unless it has been remineralized. Another option is to simply ‘cut’ or mix your tap water with RO water to reduce the silicate levels.

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Why am I getting this in my Aquarium?

The most common causes of brown algae in fish tank water are an imbalance of nutrients in a new tank, excess silicates, and excess nutrients like nitrates and phosphates. This kind of algae is very common in new aquariums and usually disappears after a few weeks.

What eats it in an aquarium?

Many aquarium algae eaters will happily feed on brown algae in fish tanks. Otos, plecos, and nerite snails are all great options for freshwater tanks. Saltwater clean-up crew like lawnmower blennies, trochus snails, and cerith snails are perfect for reef tanks.

Is it okay to have it in an aquarium?

Brown algae is usually harmless, except for extreme cases. A little brown algae in a new aquarium is perfectly normal, but abundant diatom growth in established tanks is a sign of nutrient imbalances or other problems.

Does having it mean my aquarium is cycled?

Brown algae is a sign that your tank is going through the cycling process rather than proof that cycling is complete. The best way to know if a new aquarium is cycled is to test the water parameters. A cycled aquarium will read zero ammonia and zero nitrites but show detectable nitrates.

What causes it to grow in a freshwater aquarium?

Brown algae loves fish tanks with high nitrate, phosphate, and silicate levels. Nitrates and phosphates increase as uneaten food and fish waste accumulate in your tank, and silicates usually occur in varying levels in well and tap water.

What kills it in Aquariums?

The best way to stop brown algae is to starve it by making your aquatic environment unsuitable for its needs. Simply killing the algae will not remove the cause of the problem, so avoid using any harsh chemical treatments.

Final Thoughts

Brown algae in fish tanks is something that most fish keepers will need to deal with from time to time. If you have a brown algae outbreak in a new aquarium, keep calm and allow it to work itself out. If your problem is in an established tank, run through the causes and solutions explained in this article for the best chance at removing brown algae for good!

Have you gotten rid of brown algae in your tank? Tell us about your experiences in the comments below!

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