Brown Algae in Fish Tanks: How to Get Rid of It for Good

When we talk about algae most aquarists tend to think of a carpet of green on rocks, leaves, and glass. Light and algae eaters are the usual fixes, with a dose of algicide, just in case.

But what if there is an algae that doesn’t respond to any of these solutions?

Brown Algae is an issue nearly all of us will have to deal with in the hobby and how it gets out of hand is a bit more mysterious.

Controlling it will be a real problem if you rely on the usual Green Algae methods. So let’s take some time to talk about controlling brown algae in fish tanks!

What is Brown Algae?

Brown Algae are some of the most abundant organisms on Earth, even if we usually ignore them. They are also known as Diatoms and they are found in fresh and saltwater bodies around the world.

Brown Algae are a major part of the Earth’s ecosystem. It’s estimated Diatoms produce 20-50% of the oxygen in the atmosphere, making them vital to our own survival! Their silica shells form layers hundreds of feet thick on the ocean floor where they eventually become part of limestone beds.

These tiny builders are fascinating and great to read about but not so wonderful when they get inside your aquarium.

Is Brown Algae Harmful?

Not at all! Take a look at nearly any body of water in nature and you’ll see loads of Brown Algae colonies busily photosynthesizing where Green Algae can’t. Like their green cousins Diatoms lock up free floating nutrients and produce oxygen that fish can take in.

Diatoms are more of an aesthetic problem for aquarists. The brown slimy coating their colonies form are extremely unattractive and give the aquarium a neglected appearance.

What Causes Brown Algae in Fish Tanks?

Brown Algae is the result of several conditions that nearly all aquarists have to deal with eventually. Diatoms need three things to prosper: light, silicates, and nutrients, especially phosphorus.

Light and Brown Algae

Light is hard to solve since you’ll need light to see your fish and potentially raise healthy plants. The problem here is that Diatoms evolved specifically to take advantage of low light environments where green plants and even other algae can’t live.

Some aquarist articles recommend turning off the aquarium lights to help control Brown Algae. Unfortunately, this is useless – Diatoms can live as deep as 600 feet below the surface of the water, taking in a bare trickle of light. Unless you want to wrap your aquarium in black plastic for a few weeks any ambient lighting is enough for Diatoms.

The specific type of lighting the majority of aquariums use (incandescents or low energy fluorescent bulbs) is also a problem because Green Algae and plants can’t get enough light to compete with Brown Algae for nutrients.

Paradoxically, one of the best way to control Brown Algae using light is to increase the amount of light so competitors can lock away phosphorus and nitrates.


Unlike plants and algae, which use cellulose, a complex chain of sugars, Diatoms use silicates composed of silicon dioxide (SiO2). Silicon dioxide is the base component of quartz gravel, many aquarium sands, and glass.

But wait, you might be asking! Doesn’t that mean there’s an unlimited source of silicates for Diatoms to consume? Actually, no; sand substrates or aquarium glass being a source of Brown Algae is another common myth.

Silicon dioxide’s solubility in water depends strongly on how the molecules are arranged. They are bonded so strongly in quartz-containing minerals, substrates, and glass that they are effectively insoluble (will not dissolve) in water. Glass would be a poor choice for making aquariums if water could dissolve it!

However dissolved silicates (formed from water-based reactions with silicon-containing minerals) and silicic acid are often a problem in local tap or well water sources. These agents are harmless to humans so municipal water companies don’t bother to remove it. However if your source of aquarium water is high in silicates Brown Algae is likely to be a constant issue.

Nutrients for Brown Algae

Like plants and Green Algae, Brown Algae needs several nutrients to survive, with silicates, carbon dioxide, and phosphorus being high on the list. In newly set up aquariums these nutrients can be very easy to find.

Fish food is often high in phosphorus, which mostly passes right through your fish and into the water where Diatoms can intake it. And since Diatoms need far less light than Green Algae or plants they have an easy head start in new aquariums.

Therefore, understanding and controlling the flow of nutrients is also important in dealing with Diatoms.

How Do I Get Rid of Brown Algae?

Here are a few ways that you can get rid of brown algae is your fish tank:

Chemical Additives

Unfortunately, this is the least most effective method because strictly speaking, Diatoms are not plants. Aquarium algicides have limited to no effect on them. Brown Algae can even live in chlorinated pools and other places green algae would wither.

Management through physical means and understanding the underlying chemistry are by far the best ways to remove Brown Algae from a fish tank.

Physical Methods

Brown Algae is fortunately much easier to remove physically from aquarium surfaces than Green Algae. It’s quite soft and wipes away from the glass easily with a sponge or scrubber.

The main issue is when it forms layers on aquarium driftwood, rocks, and your substrate, where it can’t be easily wiped off.

Turning over the substrate with your siphon hose can help a lot because Diatoms will grow only on the uppermost layer. By mixing your gravel thoroughly you can shade and kill most of the Brown Algae bloom.

Algae Eaters are also helpful, though it’s worth mentioning that most don’t have much taste for Brown Algae. Plecostomus may ignore it entirely however many aquarists have better luck with a shoal of Dwarf Otocinclus.

Mollies also have a taste for Brown Algae but prefer flakes over Diatoms. Algae eating specialist invertebrates like Nerite Snails are also worth trying. However it’s unlikely they will make much of an impact unless you have large numbers.

Moderating Nutrients

More often than not, Brown Algae infestations simply go away on their own! They are a natural part of the aquarium cycling process. As additional microorganisms form competing colonies the abundant nutrients Diatoms are feeding on will eventually run dry and they will disappear.

However if you have a long term or recurring Brown Algae problem, you need to consider light and nutrient issues. Can you bring in competitors for light, CO2, and phosphorus, like Macroalgae and plants?

I also recommend testing for nitrates if Brown Algae is a constant problem. The API Master Test Kit is a great option that is capable of testing for everything that you’ll need to measure.

API FRESHWATER MASTER TEST KIT 800-Test Freshwater Aquarium Water Master Test Kit
  • Contains one (1) API FRESHWATER MASTER TEST KIT 800-Test Freshwater Aquarium Water Master Test Kit, including 7 bottles of testing solutions, 1 color card and 4 glass tubes with cap
  • Helps monitor water quality and prevent invisible water problems that can be harmful to fish and cause fish loss
  • Accurately monitors 5 most vital water parameters levels in freshwater aquariums: pH, high range pH, ammonia, nitrite, nitrate

As aquariums cycle nitrifying bacteria convert ammonia into nitrite and nitrite into nitrate. However, denitrifying bacteria, which convert nitrate into gaseous nitrogen, are a little special.

They are anaerobic, meaning they can’t live where there’s oxygen. As a result sand substrates and porous rocks are perfect hiding places for these bacteria. However many aquariums don’t have the right substrate or filter medium for them to live in large numbers.

Filter media like Seachem Matrix have interior micropores where denitrifying bacteria can live free from poisonous oxygen to break down nitrates.

Seachem Matrix Bio Media 1 Liter
  • Supports denitrifying bacteria
  • Extreme surface area
  • No need to replace ever

Lastly, make sure you’re keeping up with your water changes. Free floating phosphorus, nitrates, and silicates have nowhere else to go as they don’t evaporate. Either organisms take them up or they simply build up over time.

Brown Algae is a very common problem in established aquariums where there are plenty of fish to provide nutrients but water changes aren’t being done regularly.

Using distilled or reverse osmosis (RO) water after water changes can also help control Brown Algae. These water sources are free of silicates and other minerals that Diatoms need to build their shells. However since both are pH neutral to slightly acidic (pH 5.5-7) they can cause other issues with water chemistry.

The perfect environment for Brown Algae is:

  • No anaerobic zones for denitrifying bacteria to remove nitrates
  • No plants or Green Algae to soak up excess nitrates and phosphorus
  • Dim aquarium lights
  • Infrequent water changes (which normally remove nitrates and silicates)


Brown algae in fish tanks is a common problem but easily fixed once you understand the underlying causes. Cleaning what surfaces you can, performing water changes diligently, and correcting light and nutrient imbalances are the fastest way to see success.

However for many aquarists, the best solution is to simply wait while your ecosystem balances itself out! While not very pretty, Diatoms are rarely a permanent problem.

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