Thorough Cleaning a Filter

6.8. Thorough Cleaning a Filter

Both beginners and experienced aquarium owners often make a big mistake that stresses fish in their aquarium. They give their new filters a thorough cleaning at the end of cycling. Or they clean their filters thoroughly once a month. And their water then gets very cloudy and they get ammonia spikes.

A thoroughly cleaned aquarium filter is the same as a new aquarium filter, it must be cycled for several weeks. And it normally takes months without cleaning before a clean filter will give crystal clear water. In an aquarium, in general, brown gunk is good, not bad.

“Beneficial Bacteria ain’t Pretty!”

This is long and boring. Read on only if you are a real nerd like the author. The following discussion is in layers and tends to repeat itself in more and more complexity.

Microglanis iheringi South American Bumblebee Catfish
Microglanis iheringi South American Bumblebee Catfish

The Problem with Filter Cleaning in More Depth

Many in the hobby clean their filters thoroughly once a month as they think the “brown gunk” is fish feces. Then these same hobbyists come up on social media wondering why their aquarium is always cloudy.

The surprising thing is that when informed of why their aquariums are cloudy, they almost always say they don’t believe it and that they are going to continue to clean their filters as they are just very uncomfortable with brown gunk. Ahh the power of our “cleanliness is next to godliness” upbringing.

Labidochromis hongi Red Top Deluxe
Labidochromis hongi Red Top Deluxe


Multiple replicate scientific experiments were carried out with controls. These studies looked at cleaning sponge filters. They established that:

  1. Cleaning a newly established (months) sponge filter under RUNNING unchlorinated well water OR RUNNING chlorinated water removed virtually all the beneficial bacteria
  2. Cleaning a newly established (months) sponge filter by VERY LIGHTLY SWISHING back and forth once or twice in a pail of unchlorinated well water OR chlorinated water left significant amounts of beneficial bacteria in the filter.
  3. Cleaning a LONG ESTABLISHED (years) sponge filter under running unchlorinated well water OR chlorinated water left significant amounts of beneficial bacteria in the filter.

So you never want to clean a relatively new filter media in running tap water, period.  You can get ammonia spikes. And you want to only partially clean the filter media, not thoroughly clean it. Thorough cleaning can give ammonia spikes. If the filter has been long established one can clean it often with little effect on filtration capacity.

The testing which resulted in these conclusions is shown in the following link:

6.8.1. Test of Cleaning Filters

Ctenopoma acutirostre -  Leopard Bush Fish
Ctenopoma acutirostre – Leopard Bush Fish


The best way to think of this situation is to realize that fish feces and uneaten food MUST be decomposed by a host of what are called “heterotrophic” bacteria (meaning “normal” bacteria that eat carbohydrates and proteins). The decision for the hobbyist is whether they want that bacteria to be present as cloudy water or do they want this bacteria to be present as brown gunk in the filter media. The choice is theirs to make.

Note that there is a myth that the surfaces of the substrate, rocks and the ornaments in an aquarium have significant colonies of beneficial bacteria. Unless one has an under-gravel filter this is a myth.

The substrate, rocks and the ornaments do not have “turbulent”, rapid water flow over them. “Turbulent”, rapid water flow is an absolute requirement for the growth of significant numbers of beneficial bacteria. This obviously would change if one aimed a wavemaker at the substrate to create rapid flow over the substrate.

Cynotilapia afra Cobue
Cynotilapia afra Cobue

Biofilms and Brown Gunk

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 probably the most intelligent statement any supplier of aquarium products has ever made.

Mikrogeophagus altispinosus Bolivian Ram
Mikrogeophagus altispinosus Bolivian Ram

Biofilm is the thin layer that is exposed to the flow of the water and does the biofiltration. What many miss is that this biofilm forms on brown gunk surface just as easily as it forms on the surface of the biomedia. This can be best illustrated with a cross section of a single urethane foam cell roughly 0.030 inches across (30 ppi) in a typical aquarium filter over time:

Waterflow biofilm month 1
6.8. Thorough Cleaning a Filter 12
Waterflow biofilm month 2
6.8. Thorough Cleaning a Filter 13
Waterflow biofilm month 3
6.8. Thorough Cleaning a Filter 14
Waterflow biofilm month 4
6.8. Thorough Cleaning a Filter 15
Waterflow biofilm month 5
6.8. Thorough Cleaning a Filter 16
Waterflow biofilm month 6
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waterflow biofilm description
6.8. Thorough Cleaning a Filter 18

This illustrates how the bioactivity 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. At 6 months the brown “gunk” gets enough volume to start shutting down the flow and stopping the biofiltration.

Melanotaenia lacustris Lake Kutubu Rainbowfish
Melanotaenia lacustris Lake Kutubu Rainbowfish

This concept that beneficial bacteria are in the brown gunk in filters  is not only proven by the thorough cleaning test above, there is other supporting data:

  • Diana Walstad goes into how beneficial bacteria work in her book “The Ecology of the Planted Aquarium”. She talks extensively about how the biofilms build up with a huge number of references.
  • When starting an aquarium everyone agrees that the best “seed” is to squeeze a dirty existing sponge filter into some water. The resulting brown soup can give a cycled tank in days. So obviously this is where the beneficial bacteria are.
  • K1 fluidized beds work great at keeping water crystal-clear and minimizing ammonia and nitrite readings. They only do that when they have been cycling for two to four months and build up a brown filmy mass inside the K1 media. This brown “gunk” is the reason K1 fluidized beds work so well.

Now there will be many skeptics who will say the brown gunk needs to be kept out of the aquarium and that this test wasn’t correct. I try to avoid anecdotal evidence but two comments to this website stand out:

“I’d like to say your section on filtration is excellent. I’ve kept fish since I was 7 yrs old and for the past 6 yrs have kept and bred African Cichlids. My son has a community tank in his room. When I read your article on “over cleaning filters” something clicked for me. Embarrassing as it is for me to say, I often forget about my sons tank which houses tetras and tiger barbs. When I say forget I mean, I don’t have any hands in it constantly. Without realizing it I was performing my own “test” and the results, I noticed my son’s tank was always crystal clear yet it always had the “dirtiest” filter with TONS of “brown sludge”. His fish were very healthy and NEVER got disease. Long story short, I now do my best to leave my filters alone and the difference is amazing.”

Another very similar comment was:

“This site is a nightmare. Every time I think I will spend a few minutes reading an article, I glance up and realize I’m approaching the end of my hour lunch break and I’ve not eaten anything. I have a 200L aquarium and went through a recent phase of “Why is it dirty? I must clean my filter.” which just made it dirtier. Meanwhile, in my daughters room is a 20L Endler aquarium that is spotless and has crystal clear water which I more or less ignore other than periodic water changes or the occasional test. I’ve had so many moments which I will term “eureka!” moments, where something has just clicked, so thank you very much for all your time and effort in articulating this information. It has been a real eye-opener and I am hopeful will lead to many fish both current and future having a much higher quality of life!”

Lethrinops auritus - Nkhata Bay
Lethrinops auritus – Nkhata Bay

The biggest myth about filtration is that one needs a clean filter in order for the filter to be effective. Exactly the opposite is true. The dirtier the filter media the better the filtration.  The brown gunk inside a filter is many different varieties of very beneficial organisms, including so called “beneficial bacteria”.  The filter below filtered an aquarium with perfect water parameters and some very healthy fish. It was not a “nitrate factory” nor a spewer of disease pathogens.

A Well Functioning Aquarium Filter
A Well Functioning Aquarium Filter

Now the level of this brown gunk will vary depending on the biofiltration amount. I very heavily over filter. I have huge amounts of biofiltration. The K1 media in my fluidized beds has a thin layer of light brown “gunk” on it and that is all. It never gets to the level seen in the K1 above. The foam in my FX6 filters NEVER fills with brown gunk. It is slippery, which indicates a biofilm is present on the foam. But it is not brown. It looks clean even after a year of use. I NEVER clean my filters.

Ben Ochart has one large heavily stocked aquarium which is heavily filtered with both an FX6 and a foam filled sump. His water is crystal clear. He tore down the FX6 after six months. The foam he had in the trays and the foam around the trays appeared to be “clean as a whistle”. In truth, the foam was undoubtedly covered in a clear slime of beneficial bacteria. This is the absolute ideal for any aquarium.

OB Peacock
OB Peacock

Further Data

The testing which resulted in these conclusions is shown in the following link:

6.8.1. Test of Cleaning Filters

For more information on this complex, little understood topic click on these links:

6.2. Biofiltration

6.2.1 Detritus Explained

6.2.2. Brown Gunk in the Filter

6.2.3. Cloudy Water 

Startpage Aquariumscience

Source: – David Bogert

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