Aquarium Brown Gunk

6.2.2. Brown Gunk


The “brown gunk” found in aquarium filters is all a type of aggregate called a “biofilm”; a matrix or gel of polysaccharides and proteins with bacteria, protozoans, fungi and water molds.  For purposes of this article the thin outer surface of the “brown gunk” we will call a “biofilm”. The interior of the “brown gunk” has a different bacterial population than the “biofilm” and we will simply call it “brown gunk”.


There are two main myths we need to expose here.

  • The first myth is that virtually all the beneficial bacteria in a filter media are tightly bound on the media’s surface, not on the brown gunk on the media and in between the media.
  • A similar myth, pushed by some filter media suppliers like Seachem Matrix and BioHome, is that most of the bacteria live inside “porous” media.

Exactly the opposite is the truth in both cases.  The surface of the “brown gunk” both on and between the media will have most of the beneficial bacteria, the outer surface of the media will have moderate amounts of beneficial bacteria and there will be NO beneficial bacteria INSIDE a media such as ceramic rings, lava rock, Biohome or Matrix.

Aulonocara OB Peacock
Aulonocara OB Peacock

“Brown Gunk”

All aquariums get “brown gunk” somewhere in them. Note a thin layer of “brown gunk” can be colorless. Other words used to describe this material is biofilm, “poo”, sludge, mud, waste, “yuck”, debris, detritus, mulm and “organic matter”. “Brown gunk” is much more complex than many people realize.

The many types of bacteria and organisms which are incorporated in “brown gunk” produce a very ordered structure with layers and channels that are very efficient at detoxifying and removing ammonia from the water. This structure also efficiently removes something called “dissolved organic compounds” or DOCs. This structure is largely alive, not dead. 

These tiny open channels in the brown gunk ensure that oxygen permeates very thick layers of brown gunk (like FEET of layers) via Brownian movement and diffusion. So even very thick deposits of brown gunk in something like a canister filter that hasn’t been cleaned in years will NOT go hypoxic. Hypoxic conditions give themselves away by smelling bad, very bad. And I’ve seen many filters where the brown gunk build-up is huge and there is no foul odor.

This brown gunk is epitomized by the brown gel found inside of fluidized bed media (Kaldnes of “K1”) after several months of operation. It is a thin filmy translucent brown gel.

Brown gunk in aquarium K1 media
Brown gunk in aquarium K1 media

Brown gunk is found in the pores of very open filter media like urethane foam and on the surfaces of filter media like ceramic rings. Brown gunk is NOT found inside ceramic media or media like Matrix. Brown gunk can also be found free floating in some systems where there is a low flow where it is called mulm. Brown gunk magnified looks like this:

The structure of aquarium brown gunk
The structure of aquarium brown gunk

This structure is very similar to urethane foam, very porous and easily penetrated by water. It is, of course, on a much smaller scale than urethane foam. The orange and purple bodies are beneficial bacteria (both heterotrophic and autotrophic) and the walls are mucus put out by these organisms.

Below is an electron microscope view of the brown gunk on a piece of gravel that was used in an under-gravel filter.

photo of biofilm
photo of biofilm

And here is another electron microscope photo:

photo of biofilm
photo of biofilm

Science of Brown Gunk and Biofilm

The science of brown gunk is quite complex. Technically biofilms don’t only form on the surface of the media in a filter. They form in the voids in the media and create jelly-like mucous balls of brown gunk. If the flow through the media voids is too fast the brown gunk won’t form. If the flow is too slow the various organic compounds and ammonia the beneficial bacteria are consuming won’t get to the bacteria and be removed properly. So it actually becomes quite difficult to predict the performance of media in a filter, especially with very high fish stocking.

Red Dragonblood Peacock
Red Dragonblood Peacock

There is another concept related to “brown gunk”, something called a “biofilm”. A scientist will consider all of “brown gunk” to be a “biofilm”. As mentioned above, we will consider only the thin out surface of the “brown gunk” to be a “biofilm”. This is because the thin outer layer has a different bacterial population than the inner layers.

The beneficial nitrifying bacteria in the “brown gunk” are located on the surface of the “brown gunk” in the thin but convoluted biofilm with a different bacterial composition than the body of the “brown gunk”. In an established filter media most of the ammonia oxidation is done in a thin “biofilm” which is on top of a “brown gunk”.

Peacock Blue Regal Hybrid
Peacock Blue Regal Hybrid

A “biofilm” found in fast currents or where nutrients are sparse is only 100 to 200 microns (0.004 to 0.008 inches, the thickness of a human hair) thick. And there is no “brown gunk” in such high flow areas. This biofilm can be very tenacious and virtually impossible to remove. This same thin tenacious hard biofilm will also be very slowly produced in areas of low flow, underneath a softer convoluted biofilm. 

If one has a huge amount of biofiltration one can have an invisible thin biofilm on all the surfaces. Ben Ochart has a heavily stocked aquarium with both a large sump and a foam filled FX6 on the aquarium. He took the FX6 apart after six months of operation and the foam was “clean as a whistle”. But I guarantee there was actually a very thin invisible and highly effective biofilm on all  the urethane surfaces in the foam.

OB Peacock
OB Peacock

In addition there will be a softer brown gunk which will form in areas of lower flow . This soft brown gunk (which technically is also a biofilm) will have a biofilm with a different composition on its surface.

A good example of the two types of biofilms are the two biofilms that form on a person’s teeth.

  • A soft thick grainy biofilm is what appears on your teeth if you don’t brush them for a few days. It can rapidly form. It is rough, thick and grainy. It can be easily removed with a toothbrush.
  • A thin, smooth and hard biofilm will form on your teeth over a span of months. This needs to be scraped off with steel implements and ultrasonic chisels by a dental hygienist.

The same thing happens with all filter media. A soft thick biofilm will rapidly form in weeks and a hard thin biofilm will take many months to form. The thin biofilm typically forms under a soft biofilm, much like what happens on one’s teeth. BOTH forms of biofilm are perfectly capable of oxidizing ammonia and absorbing dissolved organic compounds.

Aulonocara German Red
Aulonocara German Red

“Beneficial bacteria” (technically “nitrifying bacteria”) are only found in the top 50 microns (0.002 inches) of any biofilm. The reason for this has to do with the energy produced by oxidized ammonia to nitrate. This reaction is a very low energy reaction. Thus, each beneficial bacterial cell needs to contact and adsorb millions of ammonia molecules. This contact can only happen when there is a fast turbulent flow of water.

The beneficial bacterium thus can only grow where there is a good flow of water passing over the bacterium. As a result beneficial bacteria only grow on the surfaces of structures, not within the structures.

But if the biofilm is “grainy” and convoluted it has much more surface area than a thin flat biofilm (2x to 10x more), thus the ability of a biofilm to become significantly better when it becomes rough and old.

Peacock Red Rubin
Peacock Red Rubin
Waterflow biofilm month 1
6.2.2. Brown Gunk 26
Waterflow biofilm month 1
6.2.2. Brown Gunk 27
Waterflow biofilm month 3
6.2.2. Brown Gunk 28
Waterflow biofilm month 4
6.2.2. Brown Gunk 29
Waterflow biofilm month 5
6.2.2. Brown Gunk 30
Waterflow biofilm month 6
6.2.2. Brown Gunk 31
6.2.2. Brown Gunk 32

This illustrates how the bio-activity of the beneficial bacteria increases. The red lines (biofilm) are the ONLY areas where there is beneficial bacterial activity. It is not the volume of the brown gunk but rather it is the surface area which is important. The brown gunk is at its optimum at month five. At 6 months the brown gunk gets enough volume to start shutting down the flow and stopping the biofiltration.

This six-month time period is typical of well filtered and heavily stocked aquariums and 30 pores per inch foam. If the amount of urethane decreases the time period will decrease. Small amounts of foam in small canisters on large aquariums can get clogged in two weeks. Very heavily filtered aquariums with large amounts of foam can have the foam never get clogged.

The brown gunk/biofilm complexes which form slowly will be significantly better at giving crystal clear, clean, healthy water than ones that form quickly.

Aulonocara ngara flametail
Aulonocara ngara flametail

Not All Brown Gunk is Good

A rapidly formed brown gunk will have more heterotrophic bacteria and the fewer autotrophic beneficial bacteria and the fewer beneficial microscopic organisms.  So the faster a brown gunk forms the less desirable that brown gunk is. The slower the brown gunk/biofilm complex forms the better it will be at keeping the aquarium water crystal clear and bacteria free and the fish healthy.  Also the faster a brown gunk forms the quicker it slows down flow and has to be cleaned.

Another factor is the strength of the brown gunk/biofilm. If the brown gunk/biofilm forms fast, like in two weeks, it will be very weak and easily broken up, destroying it’s good properties. A rapidly cycled sponge filter which is taken out of one tank and put in another will take days or even weeks to regain any ability to oxidize ammonia. The mere act of moving it destroyed the biofilm structure.

A brown gunk/biofilm which formed slowly, over a period of months, is much stronger. A sponge filter which has been operating for several months typically can be switched from one tank to another with little or no impact on its ability to oxidize ammonia.

The rate at which brown gunk forms is dependent on several factors:

“Brown Gunk” build-up speed
Parameter Good Slow Build-up Bad Rapid Build-up
Food Protein Level High > 50% Low < 40%
pH High > 7.2 Low < 6.7
Filter Size Large Small
Aeration High Low

The author keeps all his aquariums in the green area, WAY into the green area! Note that adding sugar to the mix during cycling is the same as using very low levels of protein in the food and will give a very weak brown gunk/biofilm structure.

Auloncara sp Stuartgranti Galeriya Reef
Auloncara sp Stuartgranti Galeriya Reef

Cleaning the Brown gunk

Humans being humans most hobbyists clean their biomedia of all the brown gunk they can as soon as they realize some has built up in a filter. The entire concept of “cleanliness next to godliness” is so ingrained in our culture that anything “dirty” like brown “gunk” in the biomedia, must be bad and must be eliminated at all cost.

One well-meaning but inaccurate commentator said:

“If the main biological media becomes dirty or covered with slime, biological activity is significantly reduced”.

Exactly the opposite is true. The “slime” they are talking about is a thick convoluted coarse layer of biofilm with a large surface area for beneficial bacteria to populate. This is exactly what you want in your biological filter.

Aulonocara SP Super Red Ruby Peacock
Aulonocara SP Super Red Ruby Peacock

From the Poret Foam Supplier (Swiss Tropicals):

The brown filter sludge in a filter is for the most part alive and not simply waste. Removing this mud does more harm than good. The purpose of the filter media is not to filter out particles from the water as is often assumed. The media serves as the habitat for a vast array of microorganisms that include bacteria, archaea, worms, ciliates, flagellates, and many others. These microorganisms live in a community that is based on biofilms. The biofilms are created by bacteria that secret extracellular polymeric substance (EPS), which is often called “slime”. The community forms a bioreactor that processes the waste and turns it into food and energy for its members, and ultimately into organic or inorganic products that are then used by plants, evaporate, or removed by water changes. It takes a considerable amount of time to establish this “filter community”; consequently, it is very important not to disturb it unless absolutely necessary.”

This is one of the most intelligent writing any supplier of aquarium goods has produced. It is incredibly accurate in every facet it mentions. This quote is so important this is the fourth article I have put this quote into.

Aulonocara Baenschi ‘sunshine peacock’
Aulonocara Baenschi ‘sunshine peacock’

Researchers have found high flow aerated fluidized bed reactors and Kaldnes (K1) type media to be simply the best biofiltration possible. The reason for this is that K1 media will form brown adherent fuzzy films of jelly-like brown gunk on the walls of its interior. There is a high flow of well oxygenated water through the interior of these K1 media (like you see in the illustrations above) and a very good biofiltration by this “brown gunk” becomes inevitable.

Because of the constant knocking between each piece of K1 filter media as they swirl around in a fluidized bed, there never gets to be a situation where the brown gunk builds up to a point where it can stop the flow. The brown gunk always gets knocked off and disintegrated before it can get to that size. Thus, the maintenance free situation you find with K1 fluidized beds.

Aulonocara OB Peacock
Aulonocara OB Peacock

Brown Gunk Buildup and Food

There is an interesting relationship which occurs in aquariums. The amount of beneficial nitrifying bacteria, brown gunk and nitrate produced in a filter media is dependent on the ratio of carbon to nitrogen in the food. With higher carbon to nitrogen ratios there is less beneficial bacteria produced, more nitrogen containing brown gunk produced (more “assimilatory denitrification”) and less nitrate in the water.

It is thus desirable to utilize a high protein food (a low carbon to nitrogen ratio food) and to remove the more nitrates produced with more water changes. Lot of brown gunk with little beneficial bacteria in it is NOT good for an aquarium. It clogs up the filtration and slow everything way down.

Aulonocara Firefish Blueberry OB
Aulonocara Firefish Blueberry OB

The effect is considerable. A food with 50% protein will have a carbon-to-nitrogen ratio of very roughly 5.4. A food with 35% protein will have a carbon-to-nitrogen ratio of very roughly 13.5, almost two and a half times greater ratio. The 35% protein food will have large amounts of brown gunk rapidly build up, low amounts of beneficial bacteria, “dull” water and frequent ammonia spikes. The 50% protein food will have very little brown gunk buildup, a lot of beneficial bacteria, crystal clear water, and no ammonia spikes. The 50% protein food will need double the water changes of the 35% protein food.

More about this relationship can be found in the following article:

3.9. Fish Food and Gunk

There are several ways one can get an undesirable high carbon-to-nitrogen ratio. One is to use a low-protein food. Another method is to use “Stress Coat” with aloe vera gel (polysaccharides or polymerized sugars with NO nitrogen and lots of carbon). This is one reason we do NOT recommend stress coat products. 

Aulonocara Turkis
Aulonocara Turkis

In More Depth

For a better understanding of the complex topic of brown gunk and biofilms click on these links:

6.8. Thorough Cleaning

6.2. Biofiltration

6.2.1. Detritus Explained

6.2.3. Cloudy Water

2.12. Beneficial Bacteria

Startpage Aquariumscience

Source: – David Bogert

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