Enhance Your Aquarium Water Quality with Biofilter

How do you treat the water in your aquarium? By filtering it through a sieve? Stream it through activated carbon? Now those are just the most basic treatment for your aquarium.

Aquarium (thesprucepets.com)

Fish (and other aquatic pet) will eat food and excrete waste. Their waste contains ammonia that eventually will be more and more concentrated in time, and at a certain threshold, will be toxic for your pet. Ammonia could also come from another source that is organic. You may have notice that in almost every fish food packaging, there would be a warning for excessive feeding. Yes, excess feed will decay and eventually contribute to heighten your ammonia level. Another source of ammonia is dead organisms, like aquatic plant, or even dead pet that is not removed immediately after the death.

You obviously can avoid high level of ammonia by water changing, but it is by all means the most impractical way to make sure your ammonia level is safe. There is another way: by using biofilter.


Generally, biofilter is a control system of pollutant level by means of microbial degradation inside a reactor, resulting in environmentally benign material. Simple enough right? In an even simpler terms, biofilter contains microbes that could eat pollutant and convert it into environmentally safer compounds.

The term ‘biofilter’ applies to a wide variety of pollutants, not only just ammonia, but this article will be focused to ammonia-degrading biofilter.


The process involved in ammonia degrading is nitrification. Ring a bell? You might have heard it before when you studied the nitrogen cycle as basic science. Let’s bring it up again, nitrification is the biological process of ammonia (NH₃, very toxic) oxidation to nitrite (NO₂⁻, less toxic) followed by oxidation of nitrite to nitrate (NO₃⁻, even less toxic).

So, nitrification consists of two reactions: oxidation of ammonia, and oxidation of nitrite. The reactions are as follows:

Ammonia oxidation: NH₃ + O₂ → NO₂⁻ + 3H⁺ + 2e⁻
Nitrite oxidation: NO₂+ O₂ NO₃⁻ + 2 H⁺ + 2e⁻

These two reaction are performed by microorganisms, and the most common and the most studied are microorganisms from the genus Nitrosomonas for ammonia oxidation, and Nitrobacter for nitrite oxidation.

Nitrosomonas sp. (microbewiki.kenyon.edu)
Nitrobacter sp. (eol.org)


The main benefit of biofilter is of course, the removal of toxic compounds, but there are also domino effects happening because of the conversion of toxic compounds.

Water treated with biofilter will have a higher nitrate level. Nitrate is practically harmless to fish, and the same time, beneficial to the aquatic plant in your aquarium. But, this is a double-edged sword. if your aquarium has a high frequency to lighting, your aquarium may be susceptible to undesirable algae growth. While algae can be shoved off by algae-eating fish (some of them are very beautiful), this can be a serious problem if your aquatic plants can’t keep up with algae in utilising nitrate.

The way biofiltration is done — properly, fully aerated biofilter is achieved using a sparger to ensure diffusivity of oxygen to water — directly increase oxygen content in water. This way, you don’t have to worry any more about lack of aeration. Lack of aeration is a serious problem in aquarium that can result in organisms’ deaths.

A type of biofilter media, calcium carbonate-based media, have an additional benefit, i.e. pH buffer. Carbon dioxide, a product of respiration in fish, reacts with water to form carbonic acid, which can lower the pH of your water and harm your fish. This problem can easily be solved with a carbonate buffer system, which needs calcium carbonate to happen.

Carbonate buffer can maintain your pH (butane.chem.uiuc.edu)

My aquarium doesn’t have any biofiltration system, but it run well.

Your might not have installed any biofiltration system but still run without any apparent problem.

Without your knowing, your aquarium will always develop its own biofilter. How?

The microorganisms of biofilter are able to grow easily on any surfaces in your aquarium, such as its inside surface, pebbles, etc. The problem with this is, the biofilter will develop very slowly in comparison to the one that deliberately developed. In the deliberately developed biofilter, microorganisms are cultured to the media in a condition that favours well to their growth, so that the biofilter would develop quickly.

Different fish has different range of tolerance to ammonia (and some other factor controlled by biofilter). Some fish may have a wide tolerance such that it can survive the ammonia content in your aquarium before the biofiltration system has developed well. Some fish may not.

It is especially critical to new aquarium that hasn’t been used at all. The ammonia level on newly-operated aquarium can go so high and eventually kills the fishes. This is a common case for beginners in fish-keeping. More common than you think.

DIY at home

You can make yourself a biofiltration system at home using some common household tools and material.

Biofiltration unit is usually preceded by two other units, i.e. mechanical filtration, and chemical filtration. Water from tank is pumped to mechanical filter, then to chemical filter, and finally to the biological filter. You can use one vessel to contains the three units, but it is recommended to separate the units to different vessels for practical sake.

This section will cover most of the basic knowledge you need about building your own water treatment system, and will not cover the technical matters.

Mechanical Filtration

Mechanical filter strains insoluble solids from originated from the tank. Excess food, faecal particles, scales, and plant matter are some example of insoluble solids that would be filtered.

The media used for mechanical filtration are typically inert. There are several types of filtration media, some of them are pads, sponges, and filter wool. These materials have porosities that range from coarse to fine, thus allowing different degrees of filtration based on the pore size. It is recommended to use multiple layer of mechanical filtration media with descending order of coarseness so that the larger particles wouldn’t clog the fine filtration media.

There are some type of mechanical media (petcoach.co)
Different porosity of mechanical media retain different size of particles (myaquaticsolutions.com)

Chemical Filtration

While mechanical filter sieves insolubles out of the water, chemical filter removes soluble compounds which are not wanted.

The most common chemical filtration media is activated carbon. Activated carbon is filled with microscopic pores that allow adsorption of the compounds. Activated carbon is able to remove organic pollutants such as metabolic waste; organic acids; proteins; hormones; and antibiotic compounds, and also inorganic compounds from the surrounding like pesticides; nicotine; and perfumes, which enter the aquarium at the water surface.

Activated carbon can adsorb unwanted chemicals (deepblueaquariumusa.com)

Other well-known mean of chemical filtration is ion exchange resin. Ion exchange resin has more chemical filtration power and use, but costs more.

The expected output of chemical filtration is toxin-free water that can be treated biologically with microorganisms.

Biological Filtration

The media used in biofiltration has a large surface area such that it can be home for a ton load of microorganisms, ergo high conversion of ammonia.

There is numerous type of biological media that can be categorised by shape, material, size, etc. The more surface area and pores a media has, the more microorganisms that can live in it. Material consideration of the media also plays some role. For example, calcium carbonate-based media can help you to control the pH of the water.

Media that have higher surface area are usually the ones with the lightest weight, often made from plastic or rubber, so it will float in water. Floating media will be agitated more vigorously by the air pumped into the unit. Excessive agitation can result in microorganisms not being able to stick properly to the media. So having a high surface area also has drawbacks.

On the other hand, the more porous and non-plastic based media are usually way more heavier. One of the most used media of this kind is calcium carbonate ring — often called bioceramic. Bioceramic has a high amount of pores and it is made from calcium carbonate, so it can help control the pH of your water.

There are different types of biological filter media, varying in material and shape (aquascapeaddiction.com)

So when you have the biological media, how can you put microorganisms on it?

The microorganisms we need for nitrification are found on so many places such as soil, river, city fountain, etc. But there are places that have higher concentration of microorganisms, that is, established biofilter. If you have a friend that has a biofilter system, ask for some grown media and put it into your biofilter. If you don’t have any such friends, you can go to nearest river, city lake or pond, or other established body of water that has life in it, and take some sludge or soil from it.

Now that you have some starter culture, you can inoculate it by submerging the media and the starter into water. You also have to ‘feed’ them with ammonia. You can get ammonia from a broad source. You can add faeces or fish food, or you can buy ammonia-containing compound, such as ammonium chloride (NH₄Cl). You may notice that nitrification is an oxidation process, and there’s oxygen involved in the reactions. The oxygen needed by the microorganisms can be obtained from air, but since this reactions are aimed to be carried in water, additional aeration is needed. The culture must undergo aeration not only at its first inoculation, but throughout the whole usage of it.

Quality Control

When you have eventually built your whole filtration system, you might wonder whether or not your water have been treated well. There is some general parameter that can determine your aquarium’s water quality.

There are sensory remarks like turbidity, colour, foam, and smell.

Turbidity is a measure of how cloudy your water is. The cloudier your water is, the more it indicates that your mechanical filter doesn’t work properly, and you might want to take a look on it. It could mean that you have been using coarser media when the finer one is needed. Also, make sure you clean or change the mechanical media once in a while to avoid clogging and bacterial build up.

Water colour also says something about your filtration system. The most common unwanted water colour is yellow. Yellowish water indicate that your chemical filter has a problem — if you use activated carbon, it might be time to replace it with the new one. The water might turns green too. Green water indicates blooming algae in your water. Algae grows when there is enough nitrates (the product from biofilter) — and phosphate — , and enough light. Green water typically happen in outdoor pond or aquarium, and there is no aquatic plants living in it to utilise the nitrate and phosphate. While green water does not harm your fish, it impairs the visual appearance of your aquarium. You can get rid of green water by limiting the light that goes into your aquarium, and plant some aquatic plant.

Foam on your water is caused by excessive protein and other organic matter that apparently escape your filtration system. Foam is an indicator that your water is prone to bacterial infestation that can eventually harm your fish. If this happens, check your mechanical and chemical filter. A worn mechanical filter may be not sifting your water properly such that organic insoluble matter continues flow to the subsequent unit. This may also means that you have to replace your chemical filter with a new one because it is no longer able to adsorb enough organic matter.

These remarks (turbidity, colour, and foam) can also be accompanied by bad — often pungent — smell.

There are also more analytical indicator of your water, like pH and obviously, ammonia level.

When pH increases to above 9, the less-harmful ammonium will be converted to very-harmful ammonia. While pH below 6 will impair the work of the microorganisms. Therefore, it is critical to watch out for your pH. One way to control your pH is to use the aforementioned carbonate buffer which can be setup by putting calcium-carbonate gravel to your tank, or even better, using calcium-carbonate based media for your biofiltration unit. You can check the pH with simple paper-based indicator which is sold quite cheaply.

pH test paper is a quite-cheap mean of knowing your water quality (fischersci.com)

To be perfectly sure, you can more quantitatively check the ammonia level. Obviously you can bring a sample of your water to the nearest analytical laboratory, but that would be too much work. There are other easier means like ammonia test kit or ammonia alert. To employ this quantitative indicator, obviously you also have to spend more money. So if you are reluctant to spend more money after setting up the whole filtration system, good news for you that the former indicators are more than enough to inform you the quality of your water.

Ammonia alert will make you alert of your water quality (seachem.com)

Extra: Aquaponic

Aquaponic is a interconnected method of fish rearing and hydroponic plant growing. You must be remember that the output of biofilter is nitrate, and that nitrate can be utilised by plants as nutrients (in fact nitrate is one of the most important nutrient for plants).

Interconnection in nitrogen cycle between fish, microorganisms, and plants (gardendecor.us)

Clearly, there are benefits of growing your own plant with ‘free’ nutrient from your fish tank, and also cleaning up nitrate from your water.

You also can earn money by selling the vegetables you’ve grown and the fish you’ve reared! Given the fact that you don’t really need additional nutrient for your vegetables, it’s practically free (of course except the infrastructure built at the initial).

You can grow your own vegetables (nourishtheplanet.com)

Extra: Application on Aquaculture Industry

The most common application of biofiltration is the Recirculating Aquaculture System (RAS).

RAS, like the name implies, is an aquaculture system where the water is recirculated, which means there is no deliberate disposal of water. If we don’t want any water to be wasted, we should ensure the quality of the water is still in the tolerance range.

The conventional system of aquaculture utilises water from the sea directly, albeit sometimes with minimal treatment such as filtering. The problem with this system is the unpredictability of the water quality. There are a lot of activities around the sea that compromise the water quality. This system has a lot of benefit to the overall process of aquaculture, but the main benefit of this system is the controlled water quality, resulting in more consistent high quality of the product.

Recirculating Aquaculture System (http://fao.org)

It’s obviously a truism that the cost to run RAS is higher than conventional method. RAS will reach economical benefits if the products being cultured have high value and price.

Water treatment with microorganisms wields a huge power that may have been taken for granted.

This is just another story of the big power of something you cannot even see.



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