6. Filtration

Filtration is often misunderstood by those new to the hobby. They think filtration is only the removal of the particles in the water they can see, things like uneaten food and feces. They think that if these particles are removed the water will be crystal clear and healthy for the fish. Nothing could be further from the truth. The visible particle removal (“mechanical filtration”) is only a small and relatively unimportant part of filtration and does little for fish health or for crystal clear water.

Filtration should be looked at from a chart.

Filtration Options
Filtration Options

Biofiltration is obviously easily 80% of the game per this chart.

Chilotilapia rhoadesii
Chilotilapia rhoadesii

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

The Three Stages of Filtration

Most of the well meaning but ill advised advice one gets on social media is that there are three stages of filtration needed in an aquarium:

  • First layer: Mechanical filtration (removal of the large particles of food and fish waste)
  • Second Layer: Chemical filtration (removal of “toxins and heavy metals”)
  • Third Layer: Biofiltration (oxidation of ammonia to nitrate)

Mechanical filtration is a relatively unimportant stage in filtration and many, including the author, do no mechanical filtration at all quite successfully.

The major claim about chemical filtration is that is “removes toxins and heavy metals”. Just one minor problem: there are NO toxins or heavy metals in aquarium water that need to be removed. So chemical filtration only removes tannic acid, malachite green, and some smells and as such is pretty useless. 

Chemical filtration is an invention of profit driven aquarium supply companies. “Replace the cartridges containing the carbon once a month” is part of the instructions to every cartridge filter made in the past fifty years. It makes a LOT of money for filter manufacturers.

The Truth about Chemical Filtration
The Truth about Chemical Filtration

Biofiltration oxidation of ammonia to nitrate (and biofiltration of dissolved organic compounds to carbon dioxide) is very important and is the driving force behind having a filter in an aquarium.

Copadichromis azureus
Copadichromis azureus

What Science Says

Science says something different than what social media will tell you. Science says aquarium water ideally should be filtered in the following stages:

  • Mechanical filtration of the large particles of food and fish waste (a relatively unimportant task)
  • Biofilter oxidation of ammonia to nitrate by autotrophic (i.e. “eats chemicals like ammonia”) bacteria. This is a very important task. It is the major reason a filter exists in an aquarium.
  • AND, in the same media as biofiltration, biofilter oxidation of “DOCs” (“Dissolved Organic Compounds” like carbohydrates and proteins) to carbon dioxide, ammonia and water by heterotrophic (i.e. “eats normal foods like sugars and proteins”) bacteria. This DOC oxidation is very important and very overlooked. It is key to crystal clear water and good fish health.
  • AND, in the same media in the same media as biofiltration, capture and killing of things in the water like bacteria and disease pathogens by heterotrophic (i.e. “eats normal foods like sugars and proteins”) organisms like rotifers.

The last three steps go on simultaneously in the brown gunk in a filter. The filtration breakdown between the autotrophic and the heterotrophic organisms is as follows:

Biofiltration Bacteria
Biofiltration Bacteria

This give one a sense of how important heterotrophic organisms are in the filter.

This type filtration is what large intense aquaculture operations use. They use something like a rotating drum filter to remove the large particles (i.e. mechanical filtration) and then use a large biofilter (typically a K1 fluidized bed) that oxidizes both the ammonia and the DOCs. It is noteworthy that I can find NO aquaculture operation that uses chemical filtration. NONE.

Biofiltration is VERY dependent on the surface area that is available for beneficial organisms to colonize in the filter media. It is also dependent on how often the flow goes over the media. For instance, a trickle filter is roughly 30% as efficient as a submerged filter such as canister. The reason is that only 30% of the surface area of the trickle filter is under water at any given time.

Platynematichthys notatus Lince Catfish
Platynematichthys notatus Lince Catfish

Filtration Schemes

There are about as many ways to stock a canister filter, bottom to top flow hang on back filter or sump as there are aquarium keepers. This is a typical “four element” scheme:

“Typical recommended” four basket canister filter stacking

  • basket #1: small pore mechanical filter (typically polyester floss, “Pinkie pads” or 40 ppi foam) – removes some of the visible waste does nothing for the problematic ammonia and dissolved organics waste. It can significantly decrease the flow of the filter. It requires opening the filter once a week to clean or replace it. Often called “polishing filtration”
  • basket #2: chemical filtration, activated carbon – relatively useless, only makes money for manufacturers
  • basket #3: “special chemical” media – useless, only makes money for manufacturers
  • Basket #4: biofiltration media – where ammonia and DOCs are oxidized and the majority of the reason for having a filter.

This design thus devotes 25% of its media to the main reason one has a filter on an aquarium, namely biofiltration. Not a good idea in my opinion.  Also note that invariably the biofiltration media is something like ceramic rings, which testing shows is the WORST biofiltration media. 

Chindongo demasoni
Chindongo demasoni

Now as mentioned, there are thousands of “filtration” schemes used in the hobby. Another common scheme seen on social media for three basket filtration is:

  • small pore mechanical filter (typically polyester floss, “Pinkie pads” or 40 ppi foam) – removes some of the visible waste does nothing for the problematic ammonia and dissolved organics waste. It can significantly decrease the flow of the filter. It requires opening the filter once a week to clean or replace it. Often called “polishing filtration”
  • chemical filtration, activated carbon – useless, only makes money for manufacturers.
  • biofiltration media – where ammonia and DOCs are oxidized and the majority of the reason for having a filter.

This scheme devote 33% of the volume to biofiltration. Better but still not what I would recommend.

Phenacogrammus interruptus Congo Tetra
Phenacogrammus interruptus Congo Tetra

Many very good aquarists use the following scheme:

  • Basket #1: small pore mechanical filter (typically polyester floss, “Pinkie pads” or 40 ppi foam) – removes some of the visible waste does nothing for the problematic ammonia and dissolved organics waste. It can significantly decrease the flow of a canister filter. It requires opening the filter once a week to clean or replace it. Often called “polishing filtration”
  • Basket #2, #3 and #4: biofiltration media – where ammonia and DOCs are oxidized and the majority of the reason for having a filter.

This devotes 75% of the volume to biofiltration. In canisters this scheme is typified by filter floss or Pinkie pads on top of a ton of various biomedia. Typically the aquarists will use five or six types of media. This is just kind of humorous as all this biomedia only do biofiltration. They only vary in how well they do biofiltration. But note I used three to five types of media in all my many filters for some fifty years so I can’t throw any stones.

A version of this scheme is a sump with filter socks and a ton of various types of biomedia. This is a perfectly acceptable method and works well for many.

Crytocara moorii Blue Dolphin
Crytocara moorii Blue Dolphin

I now use a somewhat unique filtration method on all sixteen or so of my aquariums:

  • 100% biofiltration media (ONLY foam, K1 or plastic pot scrubbers)- where ammonia and DOCs are oxidized and the majority of the reason for having a filter.

I’m too lazy to open my canister filters (I have about six canister filters!), or to clean socks from my ten sumps, so I do NO mechanical filtration.  So I accept that I will have a 10% to 30% increase in the load of dissolved organic compounds in my aquariums. I just use EXTREMELY heavy over-filtration to handle the load. All my aquariums also have under gravel filters which I never clean.

OB Peacock
OB Peacock

Note that filtration in an aquarium is a natural process. Mother Nature is both very flexible and very forgiving. I’ve seen many different filtration schemes which have all worked very well.

One very good YouTube presenter uses only air operated sponge filters in many of his aquariums. He cleans his sponge filters thoroughly every week under running chlorinated water. His sponge filters have all been established for a long time so, as our testing showed, the beneficial bacteria in the sponge is in a very tenacious film on the foam matrix. So he doesn’t clean away or kill his beneficial bacteria. And his many aquariums of fish are very healthy and his water is crystal clear. Not the way I would do it but it works fine for him. 

Symphysodon aequifasciatus Discus Blue Rim Red Cover
Symphysodon aequifasciatus Discus Blue Rim Red Cover

Filtration in More Depth

Filtration is a very misunderstood topic because there is so much money to be made by manufacturers all claiming to make the “best filter” and the “best filter media”. The barrage of fake marketing hype is astonishing. And this get parroted on much of social media. The science of aquarium filtration can be found in these links:

6.1. Mechanical Filtration (links to aquariumscience.org)

6.2. Biological Filtration (links to aquariumscience.org)

6.3. Over-filtration (links to aquariumscience.org)

6.4. Crystal-Clear Water (links to aquariumscience.org)

6.5 Water Flow Rate (links to aquariumscience.org)

6.6. Aquaponic Filtration (links to aquariumscience.org)

6.7. Nitrate Factory Myth (links to aquariumscience.org)

6.8. The Mistake of Thorough Cleaning (links to aquariumscience.org)

Cyathopharinx foai Karilani
Cyathopharinx foai Karilani

The myth of chemical filtration is debunked in the following link:

7.4. Chemical Filtration Media (links to aquariumscience.org)

The Science of Filtration in Depth

There are some aquarium hobbyists who are interested in delving deep into the science and the calculations behind all aspects of filtration. For those who are so inclined the following is pertinent:

6.2. Biofiltration (links to aquariumscience.org)

6.2.1. Detritus Explained (links to aquariumscience.org)

6.2.2. Biofilms and Biofloc (links to aquariumscience.org)

6.2.3. Cloudy Water (links to aquariumscience.org)

Oranda Goldfish
Oranda Goldfish

When one “cycles” an aquarium one is actually cycling the biofiltration part of the filter. Thus the science of cycling is an integral part of any filtration scheme. This science is reviewed in the following links:

2.10. The Nitrogen Cycle (links to aquariumscience.org)

2.11. Inoculate for Cycling (links to aquariumscience.org)

2.12. Beneficial Bacteria (links to aquariumscience.org)

2.14. The “Mature” Aquarium (links to aquariumscience.org)


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Translated in dutch by : Joost Abrahams
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