Over-filtration in an Aquarium

6.3. Over-filtration in an Aquarium

Over-filtration is a constant topic on social media and is very misunderstood. For one thing the standard “mythology” is that a tank must have a gallon per hour flow rate that is three to ten times the gallonage of the aquarium. This mythology goes along the lines of a “600 GPH filter will filter twice the load of a 300 GPH filter”. This is simply not true.

The ability of the filter to do its job is far more dependent on the media it has in it and the effective surface area of the media than it is dependent on flow. In most canister filters a surface area of only 5 square feet per pound of fish is good enough to oxidize the ammonia from one pound of fish. The flow rate is relatively immaterial so long as it is reasonably in the range of 1 to 10 turnovers per hour.

Yellow Exochochromis anagenys
Yellow Exochochromis anagenys

But to get “crystal-clear” water it is necessary to have an effective surface area of more like 100 square feet per pound of fish. And 500 square feet per pound of fish will give absolutely amazing results, especially if the media is K1 in a fluidized bed. Again, the flow rate is relatively immaterial so long as it is reasonably in the range of 1 to 10 turnovers per hour.

Since most hobbyists use entirely ineffective media for filtration in their canisters and hang-on-back filters, they need to decidedly “over-filter” to get crystal clear water. This use of poor filtration media is explained in the following link:

7. Filter Media



When someone on social media has a huge amount of filtration this is termed “over-filtration”. The science of biofiltration says that “over-filtration” is not required for ammonia oxidation. But “over-filtration” IS necessary for “crystal clear” water. Crystal-clear water is vital to having a healthy tank. Fish in water which is “dull” or even slightly cloudy will not be as healthy as fish in crystal-clear water.

The fish’s immune system is constantly fighting all the bacteria that the gills are exposed to regardless of the type of bacteria. So a lower bacterial count means more immune system resources available for fighting off pathogens. A high bacteria concentration will compromise the immune systems of the fish and can cause any number of disease and pathogen breakouts. All owners of aquariums should strive for crystal-clear water.

Copadichromis mdoka - Mloto Reef
Copadichromis mdoka – Mloto Reef

Bacteria Count

Note that “bacteria free” is relative. A milliliter (or cubic centimeter) of dull, “normal” aquarium water will have roughly ten million, 10,000,000 or 107 bacteria. A milliliter of cloudy water can easily have one billion, 1,000,000,000 or 109 bacteria. And a milliliter of “crystal clear” water can have as little as 100,000, or 105 bacteria in it. This gives one an idea as to why reducing the bacterial count can be so effective in improving the immune systems of the fish.

If the bacteria count in the water column is low the fish can put all their immune system resource towards keeping pathogens at bay. So fish in bacteria free water are far more healthy that fish in bacteria laden water.

The Key to Good Fish Health is Clean, Bacteria Free Water

Note that, contrary to popular myth, this does NOT mean water which is changed frequently. Going from ten million bacteria to five million bacteria isn’t going to be that much help to the fish. Large water changes cannot compensate for poor filtration.

The bacteria count is related to the amount of square feet of biomedia filter media surface available to the water flow in a filter. The very rough rule of thumb is:

One Pound of Fish Needs 100 Square Feet of Biomedia Surface Area to have Crystal Clear Healthy Water

Neolamprologus pulcher Daffodil Princess Cichlid
Neolamprologus pulcher Daffodil Princess Cichlid

Over-filtration For Crystal Clear Water Explained

The most important part of any aquarium filter is the biofiltration section. The “biofiltration” is done on the surface of a substrate which is termed the “biomedia”. The greater the surface area of the biomedia the more biofiltration can be done. Biofiltration is done by two distinct groups of bacteria:

  • First rapid growing heterotrophic bacteria (heterotrophic basically means “eater of carbohydrates and proteins as food”) on the surface of the biomedia in the filter will break down the dissolved organic carbon (DOC) compounds (such as carbohydrates and proteins from waste food) in the water into carbon dioxide and ammonia.
  • Secondly, very slow-growing autotrophic bacteria (“nitrifying bacteria”) growing on the surface of the biomedia in the filter oxidize toxic ammonia into nitrate in two steps. Note autotrophic basically means “eater of chemicals (ammonia in this case) as food”. 

The first role is often overlooked as it occurs very rapidly, and these bacteria aren’t considered “beneficial bacteria” They should be considered beneficial bacteria as this portion of the biofiltration is very important in water clarity and in fish health. What is missed here is that the surface area required for this biofiltration function to give crystal clear water and optimum fish health is at least twenty times the biofiltration surface area that the ammonia-oxidizing bacteria require to be successful.

🠗 Water ContaminantAutotrophic BiofiltrationHeterotrophic Biofiltration
Ammonia and NitrateRemoves
Bad BacteriaRemoves
Pathogens like ichRemoves
Dissolved OrganicsRemoves
Feces, Uneaten FoodRemoves
Floating AlgaeRemoves
Tannic Acid, Dyes, Smells
Biofiltration Bacteria

Both types of beneficial bacteria form a thin biofilm over all surfaces. In areas with low to moderate flow the biofilm becomes, over time, a thick, slimy, porous brown gunk with billions of small channels through it. The thicker and older the brown gunk the darker the color and the slimier the feel. A dark brown slimy gunk is gold to experienced aquarists. This dark brown gunk will rapidly take any ammonia to nitrate AND remove all DOCs.

Blue Dragonblood Peacock
Blue Dragonblood Peacock

One of the best write-ups on this subject came from Swiss Tropicals, the supplier of Poret Foam. They said:

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.”

Note that this is a very convoluted intertwined process. Heterotrophic bacteria that decompose uneaten food and feces and autotrophic bacteria that decompose ammonia to nitrate are working side by side throughout the biofilters.

More often most of the “brown gunk” is in the interstices of the biofilter. Aquarists often clean their biofilters frequently to remove the “brown gunk” they think is “dirty” and “bad”. This is exactly the wrong thing to do. We go into this in more depth in this link:

6.8. Thorough Cleaning

Caridina logemanni Crystal Red Shrimp
Caridina logemanni Crystal Red Shrimp

Beneficial Bacteria don’t “Stop Growing”

Another aspect of over-filtration is the concept that beneficial bacteria stop growing when they reach a certain food loading. One well intentioned but incorrect social media commentator said:

“Having too much filtration is actually a waste. The nitrifying bacteria, commonly referred to as “BB” or beneficial bacteria colony will only grow to the size that matches its food source which is the bio-load. The bio-load obviously comes from the fish waste and any regular extra food left uneaten (which there shouldn’t be if one is feeding their fish correctly). The BB colony will grow large enough only to consume the amount of waste being produced. No more, no less. So over-filtration is technically not possible.”

This explanation goes sideways because it contains a fundamental misunderstanding about how bacteria live and multiply. Think of it this way. Beneficial bacteria take in food and multiply by dividing in two. Beneficial bacteria do not require a food source to live. They can “starve” for years with no food. They can reproduce with very little food.

Symphysodon aequifasciatus Yellow Discus
Symphysodon aequifasciatus Yellow Discus

So at a level of ammonia like 4 ppm per day the bacteria will multiply at say once every 24 hours until let’s say, for illustration, a level of one billion bacteria is reached. At that point the beneficial bacteria can handle the load and the tank is “cycled”. If the ammonia feed stopped cold at that point no more beneficial bacteria would be produced.

But with fish in the aquarium the ammonia will keep coming. So the bacteria continue to reproduce only at a slower rate. So instead of doubling in 24 hours it might take 48 hours, then 96 hours then 192 hours etc.  Three month later there might be 10 billion bacteria at the same ammonia input level, IF THERE IS SUFFICIENT FILTER MEDIA SURFACE AREA.

So, after three months, if the load of fish in the tank is doubled or even multiplied by ten the filter will have no problem handling it as far as ammonia oxidation goes.

Botia striata - Candystripe Loach
Botia striata – Candystripe Loach

Also the comment assumes that “beneficial bacteria”, i.e. autotrophic nitrifying bacteria that oxidize ammonia, are the only organisms of importance in a biofilm. As the Poret write-up alludes to, there are a whole host of “beneficial critters” in most biofilms in the aquarium, including a large volume of beneficial heterotrophic bacteria that are the organisms responsible for crystal-clear water. These organisms require a much greater surface area as explained in the section on crystal-clear water:

6.4. Crystal Clear Water

Startpage Aquariumscience

Source: Aquariumscience.org – David Bogert

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