Having brown algae in fish tanks is something all aquarists are bound to encounter at some point. Just when you think your tank is squeaky clean, the proliferation of algae happens out of the blue, without any warning.

But what many people refer to as “brown algae” is not exactly algae. So what is this dreaded brown stuff in fish tanks?

In this article, you will be walked through how to identify this brown stuff in fish tanks and what causes it to appear.

What is Brown Algae?

Anyone who owns a fish tank is aware of the risk of encountering brown algae. The dreaded brown stuff can turn the beautiful freshwater or saltwater aquariums into a hideous mess. And in spite of your cleaning efforts, it can remain a recurring problem.

It tends to be more common in new aquariums and because of this, it raises a lot of concern among beginners. So what exactly is this brown stuff in fish tanks?

Also known as Silica algae, it starts as brown spots in the fish tank and grows into a layer of dark slime that coats walls, substrate, plants, and decorations. Aquatic plants covered with silica algae cannot photosynthesize, thus they weaken and die.

On the bright side, brown algae are not dangerous to fishes and this problem is a cinch to solve once you determine the cause. Plus, there are a few preventative measures you can exercise to help keep your aquarium squeaky clean and algae-free.

– Brown Algae Is Not Algae

The reason why many hobbyists fail to eliminate brown algae growing in fish tanks is that they employ methods that are only applicable to real algae. Here’s the kicker ━ brown algae is not a species of algae, but a clumpy patch of interlocked single-celled organisms called diatoms. To put it simply, it is a bacterial colony.

“Brown algae” is merely a layman’s term that refers to the Class Bacillariophyceae. These unicellular microorganisms are invisible to the naked eye, but they can be found in almost any aquatic environment. You won’t notice these critters until they explode in huge numbers. Since diatoms can’t swim around, they would simply attach themselves to nearby surfaces.

While diatoms are not a species of algae, they are still getting lumped in with algae because of their similarities. These organisms:

  • need light to thrive
  • feed on organic wastes like nitrates (NO3-) and phosphates (PO4)
  • have a soft, slimy structure

What makes brown algae different from real algae is its requirement for silica (SiO2). Silica, also known as silicon dioxide, is a natural compound made of silicon and oxygen. This compound is abundant in aquatic environments and many forms of rocks, such as sandstone and quartz. Diatoms feed off silica and use it to build a wall to protect themselves.

– Brown Algae vs. Blue-Green: How Do They Differ?

The quickest way to identify brown algae or silica algae is to look at the color. Brown algae appear rusty brown or mustard, especially under artificial lighting. If you rub a little piece off your glass using your fingertip, it would feel grainy.

While there can also be brown algae in saltwater tanks, there is also something called cyanobacteria that looks similar to diatoms and is peculiar to saltwater environments. Cyanobacteria appear greenish and slimy with an odor to boot.

Commonly known as blue-green algae, they are unicellular organisms that can form colonies. Cyanobacteria can grow rapidly in reef tanks, especially when there is a buildup of waste and excess nutrients due to overfeeding or irregular water changes.

Blue-green algae are common in reef tanks that have yet to establish beneficial bacterial colonies, but they may also appear in a mature aquarium.

With cyanobacteria, you can grab a piece and they come off in big sheets. While it is quite tempting to disturb them, you might only end up pushing them to colonize other parts of your tank.

What Causes Brown Algae?

Identifying the root cause of the proliferation of brown algae is a crucial step to help you win your battle against them. So let us go through the four possible reasons behind this problem.

– Silicates

The excess of silicates is often the number one reason why there are brown algae in freshwater aquariums, particularly in new setups.

Adding a new sand substrate — especially play sand, blasting sand, and other silica-based sand mixes — causes a huge spike in silicates. Live rocks cause silicates to leech into the water as well, thus providing diatoms an all-eat-you-can buffet. Tap water and well water also increase the odds of a diatom bloom since these waters are high in silicic acid.

When food is abundant, the diatoms will thrive and proliferate rather quickly. So if the problem is due to excessive silicates, you will need a special silicate-absorbing resin for your tank’s filter. The diatoms should die off due to the lack of food, but it may take weeks to see a difference.

– High Nitrates

The rust-colored algae in a fish tank may also indicate that nitrates are getting out of hand. Nitrate is a by-product of nitrite oxidation during the earlier stages of the nitrogen cycle. This waste product is present to some degree in all home aquariums. It comes from food leftovers, decaying plant matter, fish waste, and plant fertilizers.

Compared to ammonia and nitrite, it is far less toxic to fishes but it can still stunt the growth of your pets and make them more prone to disease. Therefore, you will want to test your tank’s water regularly. Keeping nitrate levels low is a vital step in maintaining a healthy aquarium. Ideally, you will want to keep the levels at less than 20 ppm.

You may also add these fast-growing plants to your aquarium:

  • Anacharis Elodea
  • Duckweed
  • Echinodorus bleheri.
  • Frogbit
  • Moss Balls
  • Water Lettuce
  • Water Sprite
  • Vallisneria Spiralis

Plants absorb the nitrates in water, which is needed for their healthy growth and keeps the balance in your aquarium.

– High Phosphates

Phosphates are another major contributor to algae outbreaks. As food debris, rotting plants, and fish waste break down, they generate phosphates.

All aquariums have some degree of phosphates, as every living being needs this nutrient. While phosphate is a part of life, too much of it fuels diatom and algae blooms that can deprive the water of oxygen.

Maintain ideal phosphate levels by performing water tests regularly. Aim for the following:

  • Freshwater aquarium: 0.5 – 1 ppm
  • Planted freshwater tank: 1.5 – 3 ppm
  • Reef tanks – 0 – 0.03 ppm

Brown algae will thrive in both freshwater and marine tanks as long as there is a source of food. Some city tap water can have an extremely high phosphate content, making diatoms and cyanobacteria more likely to grow.

– Too Much Lighting

There is a tremendous amount of controversy on the Internet regarding brown algae. Some hobbyists say too much lighting causes it, while others say the exact opposite. Which one is the correct explanation? The truth of the matter is:

  • Light will always be a driver of plant and algae growth regardless of the circumstance.
  • Decaying organics, a lack of tank maturity (bacterial balance), and insufficient plant biomass also contribute to this problem.

So does more light mean more algae? The short answer is YES!

How to Get Rid of Brown Algae

Listed below are simple yet effective techniques to get rid of brown algae in fish tanks. As soon as you have determined the cause of the problem, you can match it with the correct solution.

– Perform a Large Water Change

Changing out the tank water eliminates a large percentage of nitrates and phosphates that diatoms eat to survive. Make a habit of doing water changes once a week to keep brown algae at bay.

– Remove Brown Algae from Tank Walls

Removing brown algae from tank walls is not an arduous task regardless of whether your tank is made of glass or acrylic. No scrubbing is necessary since diatoms don’t adhere strongly enough to smooth surfaces.

While an old cloth will do, I prefer to use a small squeegee. I guarantee it will give you the most success!

– Remove Brown Algae from the Substrate

The technique needed for this step will be determined by the type of substrate you use ━ gravel or sand.

  • For pebbles or gravel

You can remove large pebbles and rinse them off separately. For gravel and smaller pebbles, you can use a siphon vacuum.  You will want to push the tube down into the gravel so the diatoms can get sucked out through the hose.

  • For fine sand

Removing brown algae from fine substrates can be a tad trickier since there is a high chance that the particles can get sucked up into the siphon.

Then again, not all sand substrates have the same texture and density. If you are using ultra-fine substrates, they will suck up more easily in your siphon and you will have to add more sand in your aquarium.

If your substrate is super fine, you will not want to stick your siphon tube into it too deeply. Use the tube to swirl the water above the sand and suck up detritus that floats up into the water column.

The best thing about this method is that you are not disturbing your aquascape. The sand remains undisturbed. You may also use a chopstick to stir up the substrate and hover above your siphon to vacuum whatever gets loosened.

  • For heavier sand

If you use heavier sand and you wish to deep clean your substrate, gravel vacuuming is the way to go. Stick the tube about an inch into the sand and suck up the waste.

– Scrub Brush Algae Off Plants and Ornaments

Remove rocks, fake plants, and other decorations from the tank and clean them separately. Soak the ornaments in a bleach solution (½ cup of bleach per gallon of water) for 10 to 20 minutes. Use a scouring pad to rub off any remaining algae before rinsing the objects with running water.

As for plants, you want to be more careful. Remove the plants and gently wipe down the leaves using a soft sponge.

– Get Fish that Eat Brown Algae

Everybody likes the idea of having a “clean-up crew” but bear in mind, you will have extra critters to care for once the algae are gone. A single pleco, snail, or shrimp won’t be able to clean up every last bit of algae, which means you will get at least a small group of algae-eating animals.

– For a Freshwater Aquarium

  • Nerite snails

Nerite snails are one of the most popular aquarium snails in the hobby, especially among beginners, since they are low-maintenance. These peaceful critters are also safe to keep with live plants, shrimps, and any type of fish.

The snails would spend most of their time moving around and eating phytoplanktons. Against blue-green and brown algae, these critters are unmatchable! What’s more, Nerite snails can thrive both in freshwater and saltwater.

These snails are quite incapable of reproducing in freshwater, which is good news since you also don’t want them to overpopulate your freshwater tank. As they are popular, you can find them almost always available at local pet stores and chain stores.

  • Amano shrimp

Amano shrimps are the most efficient when it comes to eating algae. These critters aren’t picky eaters and will graze almost any type of algae, including red algae and black beard algae. You will find these shrimps constantly grazing. The only downside is that they tend to go underneath the substrate, so take that as a warning if you have newly planted ground-covering plants.

  • Plecostomus species

Also known as the “janitor fish”, plecos can help clean tanks as they are natural scavengers. These bottom-feeders will nosh on leftovers that would otherwise cause nitrates to spike up.

While they may eat brown algae, you can’t expect your suckermouth fish to feed on brown algae all the time. They also might not be keen on them, especially when there is more appealing food nearby.

– For Saltwater/Marine Tanks

  • Trochus snails

Not only are these snails great at cleaning up brown algae off the rocks and aquarium glass, but they also add a pop of color to your tank. Trochus snails come with a beautiful, conical shell that has been prized by jewelry makers.

  • Mexican Turbo snail (Turbo fluctuosa)

The Mexican Turbo snail is another valued member of your marine tank’s cleanup crew. These snails consume diatoms off of live rocks, substrate, and tank walls. As a nocturnal species, they are more active at night.

How to Prevent Brown Algae from Recurring

Your pet fish may not care about brown algae and will swim happily in their tank, but you don’t want that brown gunk sitting too long, especially in reef tanks and planted tanks. Diatoms aren’t as forgiving to your fishes’ environment. Here’s how to prevent diatom blooms from going out of hand.

– Use a Filter that Is Rated for the Size of Your Tank

While it may sound pretty obvious, I have seen new hobbyists use the wrong filter for their tank time and again. If your filter is not up to snuff, then it is very likely that brown algae will make a comeback.

Your filter should be able to cycle your tank’s water at least four to five times per hour. Equally important, your filter should provide three stages of filtration: mechanical, chemical, and bacterial filtration. Adequate filtration plays a crucial role in maintaining good water quality and of course, healthy, happy fish.

– Increase Water Flow

Diatoms prefer stagnant water, so you may want to add additional powerheads to make sure there are no dead zones. With increased water flow, brown algae can’t easily anchor onto surfaces.

– Keep Up with Aquarium Maintenance

Keeping the aquarium pristine and performing partial water changes once a week is the best preventative measure. Weekly water changes eliminate the nitrates and phosphates that brown algae need to thrive.

– Don’t Overfeed Your Fish

Overfeeding is often the main culprit of excessive amounts of nitrates and phosphates in the tank water. Most fish don’t need to eat more than two feedings a day and you should limit the feeding time to about three to five minutes.

Uneaten food that has sunk to the bottom will produce a ton of nitrate and phosphate. Even if your fish does eat all the food offered, they will produce a ton of waste, with similar results.

– Use a UV Sterilizer

UV sterilizers can be expensive, but they are a worthwhile investment. The UV light can kill diatoms, bacteria, and some viruses that could otherwise cause disease.


Be aware that brown algae may return if the underlying cause is not corrected. While it may never be eliminated 100%, there are several things you can do to keep it at bay. So before you go, here is a summary:

  • Too much lighting combined with poor distribution of nutrients can lead to brown algae growth.
  • Brown algae may also indicate that something is off with the parameters.
  • Nitrates and phosphates are prime contributors to this problem. Perform regular tests to keep the nitrate and phosphate levels within the ideal range.

Diatom blooms are common in new tanks, so don’t worry too much about them. Consider it as a hobbyist’s rite of passage!

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