Optimize Your Biofilter: A Guide to Ideal Biological Filtration

Optimize Your Biofilter A Guide to Ideal Biological Filtration

Biological, mechanical, and chemical filtration – the terminology can be confusing for aquarists just starting in the hobby. The different types of filtration all play important roles in maintaining proper water quality and a healthy environment for aquatic animals and plants.

Of course, many aquarists might confidently say that they know about the nitrification process. But what if I told you that, apart from Nitrifying bacteria, there are also Heterotrophic bacteria that should be considered beneficial? I’m certain that for many, even seasoned aquarium keepers, this might be a new revelation!

This article will explain what biological filtration is, how it works, and why it is an essential (actually, the most important) part of any aquarium system. I’ll also discuss methods for optimizing the biofilter to keep aquarium inhabitants happy and safe.

What is Biological Filtration?

NitrogenCycle_DiagramA Biological Filter (or Biofilter) is not a physical device, it is a system for creating and maintaining colonies of beneficial bacteria (Nitrosomonas and Nitrobacter bacteria – nitrifying bacteria) to convert harmful substances like ammonia, into nitrites, and nitrites into nitrates.

This process is also called the nitrogen cycle.

The vital activity of all organisms inhabiting the aquarium (such as waste), as well as the decomposition of organic matter, leads to the formation and accumulation of extremely toxic substances. Therefore, a process called biological filtration is used to process them into less harmful compounds:

  • Ammonia is first converted into nitrite by Nitrosomonas bacteria. Ammonia and nitrite are highly toxic.
  • Then Nitrites are converted into nitrates by Nitrobacter bacteria, which is less harmful at lower levels.
  • Aquarium plants absorb some nitrates, while the remaining ones are removed from the aquarium through regular water changes.

Ammonia nitrite nitrate formula

Heterotrophic Bacteria as Biological Filtration

Most aquarists think nitrogen cycling via nitrifying bacteria is the only form of biofiltration.

This is not completely so.

In reality, there is another crucial process at play – the removal of dissolved organic carbons (DOC), which is taken care of by a group of heterotrophic bacteria.

DOCs consist of a complex mixture of compounds like proteins, acids, humic substances, etc.

Sources of DOCs include:

  • Fish, invertebrate, and plant waste (feces, excretion)
  • Uneaten food and decaying organic matter
  • Natural organic substances released from substrates, wood, leaves
  • Tap water can also contain DOCs, etc.

The metabolic activities of aquarium inhabitants, as well as the decomposition of organic matter, produce dissolved organic compounds and ammonia simultaneously.

In most cases, both DOCs and ammonia originate from the same fundamental processes – the production and breakdown of organic substances in the aquarium. They are closely interrelated water quality parameters.

Nitrifying bacteria cannot remove dissolved organic carbons from the water. It’s actually the job of heterotrophic bacteria to handle this important task.

Heterotrophic bacteria rely on organic carbon compounds (like fish waste, uneaten food, fungi, protozoa, floating algae, etc.) as their source of energy and nutrients. Unlike nitrifying bacteria, which can use inorganic compounds like ammonia or nitrite as their energy source, heterotrophic bacteria feed on DOC.

In simple words, heterotrophic bacteria convert organic substances into ammonia, which are further processed by other bacteria in the nitrogen cycle.

Benefits of heterotrophic bacteria:

  • Improve water quality and clarity by rapidly breaking down and consuming dissolved organic compounds like proteins and acids that would otherwise cloud the water and accumulate.
  • By processing organics, these bacteria prevent the growth of other bacteria in the water column that could make animals sick.
  • Outcompete and exclude pathogens and fungi that could colonize the filter and infect the aquarium.
  • Their rapid metabolism prevents excessive buildup of organics and allows them to process contaminants in a single pass of water through the filter.

Where Do Beneficial Bacteria Located

Everything about Beneficial Bacteria in AquariumsNitrifying and heterotrophic bacteria inhabit different areas and surfaces in the aquarium based on their needs:

Nitrifying bacteria:

  • Primarily located in the filter media,
  • Substrate,
  • Aquarium walls,
  • Driftwood,
  • Plants, etc.

Practically any surface in an aquarium is a substrate for beneficial bacteria.

At the same time, objects with a porous structure (for example, sponges, bio-balls, highly porous ceramic rings, etc.) will inherently contain a higher concentration of these bacteria due to their increased surface area. This is why, even though these bacteria can thrive on various surfaces within the aquarium, their main concentration will be on the filters.

Aerobic and anaerobic heterotrophic bacteria:

  • Anaerobic. Found in deep substrate (oxygen-depleted zones).
  • Aerobic. Filter media (as the brown gunk).

Note: Although the brown gunk can be found on the surface of the substrate and beneath it, in most cases, this is the result of poor aquarium filtration and aeration. If you have bottom-dwelling animals, it’s better to remove them.

To perform their role effectively, aerobic heterotrophic bacteria should have a significantly larger surface area compared to nitrifying (at least 1:10).

Main Factors Affecting Biological Filtration

Biological filtration relies on colonies of beneficial bacteria. There are several key factors that impact the efficiency of the biofilter:

1. Surface Area

As mentioned earlier, the porosity of material structures has a significant impact on the quantity of beneficial bacteria that can inhabit them.

With the maximum surface area, we can get huge colonies of nitrifying bacteria. This makes intuitive sense – more surface area provides more attachment sites and living space for the bacteria.

However, research has also shown there is a point of diminishing returns with extremely porous media. Materials like sintered glass or plastic bio-balls with microscopic pores and crevices boast surface areas of 800-1200 m2/L or even higher.

According to the studies, increasing surface area over 500 m2/L does not necessarily improve the biofiltration capacity or efficiency. The problem with extremely small pores (smaller than 0.5 mm) is that it restricts water flow and hinders the diffusion of oxygen deep within the pores. Thus, the inner areas become oxygen-depleted dead zones.

The ideal balance is media that maximizes livable surface area while maintaining good water movement and oxygenation.

Moderately porous media with pore sizes of 1-2 mm, such as ceramic rings, lava rock, or plastic bio-media, provide ample surface area for robust bacterial colonization while allowing sufficient water flow and oxygen penetration throughout the media.

2. Media Volume

The amount of biological filter media needed for an aquarium depends on 2 key factors:

  • the total water volume,
  • the stocking level (bioload).

Bioload refers to the waste output of the fish, snails, crabs, crayfish, frogs, and other inhabitants in the tank. For example, heavily stocked tanks with large animals or dense schools of small fish have a higher bioload. As a result, they require more filter media to process the increased ammonia and nitrite.

We live in an extremely commercialized world where we are constantly being pushed to buy products that do not align with reality. Some filter products may claim their compact media cartridges can handle even large tanks.

Well, perhaps this might work with tanks that have few animals. However, I would never consider doing this with heavily stocked aquariums.

This is especially important during spikes in ammonia and nitrite, which occur when first cycling a new tank or after adding many new fish at once.

When the biofilter is undersized for the bioload, the bacteria colonies won’t be able to handle it in time. This will stress animals and can even cause losses.

For this reason, it is best to choose a filter rated for a larger tank than you actually have. Ideally, filter media should fill at least 1/2 to 2/3 of the filter chamber.

For example, if you have a 10-gallon (40 liters) tank, choose the filter, which is rated for at least 20 gallons (80 liters). The difference in money is minimal but the benefit is huge!
3. Water Flow Rate and Oxygenation

Many aquarists still believe that biological filtration requires flow rates as high as 10 times the tank capacity per hour or higher. It is supposed that fast water flow provides more oxygen and ammonia to the beneficial bacteria.

However, scientific studies have shown that there is a maximum threshold for water turnover where further increases in flow rate do not improve nitrification.

The minimum recommendation is 2-3 times the volume per hour.

In the book “Aquatic Systems Engineering: Devices and How They Function” by P.R. Escobal, a calculation method is presented that takes into account the fact that when water exits the filter and re-enters the aquarium, it mixes with the rest of the water.

So to filter the entire tank volume, the filter needs to process about 9.2x the total water volume. This ensures approximately 99.9% of the water gets filtered.

The formula to calculate single-pass filtration time is:

(Aquarium volume x 9.2) / Filter flow rate (L/hr) = Hours for 1 full turnover
Then to get the number of turnovers per day:
24 hrs / Single-pass time = Turnovers per day

For example:

– 150 L aquarium (90x45x45 cm)
– Filter flow rate 360 L/hr
(150 L x 9.2) / 360 L/hr = 3.83 hrs
24 hrs / 3.83 hrs = 6.26 turnovers per day

So for this aquarium, the filter processes the entire water volume about 6 times per day.

By using this calculation, you can check if your filter provides sufficient turnover for the aquarium size and stocking level. Faster turnover may be needed for larger bioloads.

Note: Generally, aquarium filters are designed to exceed this minimum flow rate. Most filters today provide a turnover of at least 5-6x per hour, which is adequate water circulation for biofiltration in the average home aquarium.

Increasing flow beyond these levels does not significantly enhance the bacteria’s waste processing capacity. The bacteria’s metabolic rates remain limited by oxygen availability rather than water flow.

Important: Without a supply of fresh, oxygen-rich water, bacteria will quickly die. Instead of beneficial nitrifying bacteria, anaerobic microorganisms will colonize it, which may start producing hydrogen sulfide and methane. If you start a filter that has been turned off and stagnant for many days without rinsing it, it can lead to animal poisoning.


Nitrifying bacteria thrive best within an optimal temperature range of 77-86°F (approximately 25-30°C). This temperature range accelerates their metabolism and reproduction, speeding up the nitrogen cycle.

Colder temperatures outside of this zone significantly slow down the bacteria’s waste processing capacity. For example, at 50°F (10°C) growth of nitrifying bacteria decreases by 75%. Extremely high temperatures above 35°C/95°F will inhibit their growth.

Sudden and drastic temperature fluctuations can also crash the tank, as the bacteria cannot adapt their metabolism quickly enough.

Keeping nitrifying bacteria in their comfort zone ensures an efficient nitrogen cycle.

Important: Keep in mind that the relationship between temperature and oxygen solubility follows a general trend: as water temperature increases, its ability to hold dissolved oxygen decreases.

Biological Filtration, Plants, and Water Changes

It is important to remember that nitrates, (the end product of organic decomposition), cannot be removed by beneficial bacteria from the water and gradually accumulate.

In classical aquariums, there are only two ways to remove nitrates:

  • aquatic plants,
  • water changes.

Note: Anaerobic bacteria (Heterotrophic bacteria) can do that but they will require a special setup with deep substrate.

Therefore, biological filtration should never be considered a replacement for water changes. Regular water changes are essential regardless of the type of biological filters in use.

For example, in fish tanks, it is recommended to perform water changes of at least 20-30% of the aquarium volume once a week. In shrimp tanks, we can do 10-15% water changes, since they do not produce a lot of waste.

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Troubleshooting Tips

If you experience elevated ammonia or nitrite levels, there are several potential causes to check:

  • Insufficient surface area. Upgrade to more porous media like ceramic rings.
  • Too little media volume. Fill at least 2/3 of the filter chamber.
  • Low oxygen. Improve water circulation and surface agitation.
  • Cold temperatures. Raise temp gradually to the ideal range for the beneficial bacteria.

Quick Comparison of Biological Filtration Systems

How to Set Up a Crayfish Tank - filtersWhile biofiltration can occur in any aquarium setup, some filters are better optimized for it than others. Next, I will provide a comparative analysis based on my experience.

  • Canister filters. They provide large media volumes and customizable flow rates ideal for biological filtration.

Efficiency (Rating: 9/10)
Ease of Maintenance (Rating: 7/10)
Cost (Rating: 6/10)

  • Hang on the back filters. HOB filters offer simplicity but more limited space and flow control. Supplement with added media like porous bags.

Efficiency (Rating: 7/10)
Ease of Maintenance (Rating: 8/10)
Cost (Rating: 8/10)

  • Sponge filters. They provide surface area but minimal mechanical filtration.

Efficiency (Rating: 6/10)
Ease of Maintenance (Rating: 9/10)
Cost (Rating: 9/10)

  • Sump filters. They also excel due to massively customizable filter compartments separate from the main tank. These filters are usually used in marine tanks or very large freshwater aquariums with heavy bioloads. They can provide efficient biological filtration and help maintain stable water parameters.

Efficiency (Rating: 8/10)
Ease of Maintenance (Rating: 7/10):

Cost (Rating: 6/10)

  • Fluidized Bed Filters. These filters create an ideal environment for beneficial bacteria to thrive. They are exceptionally efficient at removing ammonia and nitrites. However, they are not as common as the other filter types.

Efficiency (Rating: 8/10):
Ease of Maintenance (Rating: 7/10)
Cost (Rating: 7/10)

In Conclusion

Biological filtration is the most critical type of filtration for maintaining a healthy aquarium environment.

Optimizing conditions for nitrifying bacteria growth is critical for efficient biofiltration. This includes providing adequate surface area, media volume, water flow, oxygenation, and ideal temperature range.

However, in most cases, biological filtration alone is not sufficient – regular partial water changes are still required to dilute accumulating nitrates and replenish trace elements.


  1. Escobal, P.R. Aquatic Systems Engineering: Devices and How They Function. Dimension Engineering Press, 2000.
  2. Hovanec, Timothy A., and Edward J. DeLong. “Comparative Analysis of Nitrifying Bacteria Associated with Freshwater and Marine Aquaria.” Applied and Environmental Microbiology, vol. 62, no. 8, 1996, pp. 2888–2896. 
  3. Spotte, Stephen. Seawater Aquariums: The Captive Environment. John Wiley & Sons, 1979.
  4. Diana L. Walstad, “Ecology of the Planted Aquarium: A Practical Manual and Scientific Treatise for the Home Aquarist”, 1999, p.63.

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