Aquarium Filtration Guide (2023 FAQ)

Why is filtration necessary?

Why filter the water? The answer is quite obvious when one considers what happens in an aquarium. A fish is a living organism; it eats, excretes in, and “breathes” from the water that surrounds it.

What is the biology of the aquarium?

Fishes waste products may be solid (eg faeces) or dissolved (eg urine, excess salt excreted from the gills). Solid waste is predominantly made up of organic carbon compounds. Heterotrophic bacteria feed on these, consuming oxygen and producing carbon dioxide. Without adequate oxygenation this process can cause problems, however, most aquarists wish to remove solid wastes simply because they are unsightly. Solid wastes are removed primarily by mechanical filtration. While this clears the water it should be remembered that the solid wastes are not truly removed (and will still be consuming oxygen) until the mechanical filter media is cleaned or replaced.

Dissolved waste products contain nitrogen in the form of ammonia and urea, which is also broken down into ammonia. In water, ammonia exists in two forms: Compound ammonia, NH₃, and the ammonium ion, NH₄. It is common for these to be referred to collectively as “ammonia”; however, it is the NH₃ form that is of greatest concern to aquarists. Ammonia in the ionic state (ie NH₄) is relatively non-toxic, while the compound ammonia (ie NH₃) is highly toxic to fish. The proportion of dissolved ammonia that exists as NH₃ depends on the pH of the water (a higher pH means more NH₃) and, to a lesser extent, the temperature. Therefore, at higher pH, ammonia is more likely to cause problems.

In an aquarium, as in nature, ammonia is oxidised by aerobic nitrifying bacteria such as Nitrosomas spp and Nitrospira spp. Nitrosomas spp. oxidise ammonia to nitrite (NO₂). Nitrite is still toxic to fish, although less so than ammonia. Nitrite is then further oxidised to nitrate (NO₃) by Nitrospira spp. (Note, oxidation of nitrite in aquaria was formally thought to be carried out by Nitrobacter spp, but recent evidence suggests that Nitrospira spp play a larger role than Nitrobacter in aquaria). Nitrate is less toxic than both nitrite and ammonia, although different fish have different sensitivities to nitrate, some being susceptible to nitrate poisoning and some being highly resistant. Corals and many invertebrates are sensitive to nitrate levels.

Nitrosomas and Nitrospira are present in every aquarium. They are present in low numbers in the water but are mainly found on surfaces: on the glass, on rocks, plants and ornaments, and in the gravel. Wherever there is sufficient oxygen, these bacteria will be carrying out the oxidation of ammonia and nitrite. Therefore, every aquarium has some degree of biological filtration. However, in order to keep more than a few hardy fish in an aquarium, a greater number of these bacteria are needed, and they must be supplied with a constant flow of oxygenated water. This is the aim of biological filtration.

Since Nitrosomas and Nitrospira will grow on any suitable surface most filters designed for mechanical or chemical filtration will also provide some biological filtration. Biological filtration will be impaired, however, by the presence of organic wastes, as heterotrophic bacteria will use up the available oxygen before the nitrifying bacteria. Where a heavy load of organic waste exists, conditions can become anoxic (without oxygen), and biological filtration will cease altogether. In the worst case, anaerobic sulphur fixing bacteria will start producing extremely toxic hydrogen sulphide.

For this reason, mechanical filtration media should be cleaned or replaced regularly. Clearly, if the filter media is replaced, its biological filtration ability is lost. The best way to achieve efficient biological filtration is, therefore, to have a biological filter media which is not replaced and which does not collect organic waste, or which can be regularly cleaned of organic waste without harming the desirable nitrifying bacteria.

How much filtration is required?

Clearly, water must be moved through the filter medium (whether mechanical, chemical or biological) for it to be effective. More water flow means more filtration, at least to a certain extent, but filtration also depends on the surface area and volume of the filter media. The greater the surface area and volume of media the greater the filtration ability. This is true for mechanical, chemical and biological filtration. For “good” filtration the entire aquarium volume should be passed through suitable filter media at least three times an hour for cold water and tropical tanks. For marine tanks greater turnover is needed, at least five times an hour is recommended. The flow rate can be less than this where a large volume of media is used, eg in canister filters.

Greater water turnover than this is recommended in smaller tanks (where there is a lesser water volume to dilute toxic waste products), or where the types of fish being kept are large and/or messy.

By far the most common method of moving water is the magnetic impeller driven pump. These pumps are silent and efficient, and economical to run. An air pump can also be used to move water: as air bubbles rise they draw water up with them, creating circulation. However, the water turnover that can be achieved with an air pump is small compared with the output of most impellor driven pumps. Other disadvantages of air pumps are noise, even the quietest air pumps are far from being silent, and cost since most air-driven filters require frequent changes of filtration media.

What is the role of water changes?

The final product of a biological filter is, as mentioned previously, nitrate.

In nature, nitrate is consumed by algae and plants, producing plant tissue, and by anaerobic bacteria, producing nitrogen gas (N₂) that escapes to the atmosphere. In an aquarium, these bacteria are not generally present, and conditions are rarely suitable for the reduction of nitrate to nitrogen gas. Additionally, many aquatic aquarium plants are unable to use nitrogen in the form of nitrate, and so nitrate tends to build up in an aquarium.

Excess nitrate in an aquarium is undesirable because of its potentially toxic effects and the fact that it will promote the growth of algae and possibly damage desirable aquatic plants.

Nitrate can be removed from the water, but methods of removal are not practical for most aquariums. Denitrators remove nitrate by reducing it to nitrogen gas using anaerobic bacteria, but these are generally slow, expensive and inefficient. There are also chemical filter media that absorb nitrate, but again they are relatively expensive and inefficient. Algal scrubbers can be used; these consist of a shallow, brightly-lit aquarium full of algae through which the water is pumped. They are expensive and relatively difficult to set up, and while they are invaluable in, for example, extremely large recirculating systems, they are not practical for most home aquariums.

The only method of removing nitrate which has proven successful in-home aquaria is that employed in some marine reef aquaria which utilise organisms that colonise the rockwork and sand (often called “live” rock and sand, respectively). Crevices in the rock, and/or a deep bed of sand provide low-oxygen environments that can harbour de-nitrifying bacteria, allowing the breakdown of nitrate to occur. Water circulation moves water past these organisms and prevents annoxia (complete absence of oxygen). While this method has been used successfully, it may be difficult to establish, and cannot be used in freshwater. This system is usually used in combination with protein skimming, which also helps to slow the production of nitrate.

In most cases, the easiest and best way to remove nitrate is with regular partial water changes. Partial water changes will also help to stabilise pH, remove other organic wastes and replace a range of lost trace elements.

For these reasons, however good your filtration is, partial water changes are always necessary.

What are the dangers of overfeeding?

As aquarists, we have all at some stage been warned not to overfeed our fish. Why is overfeeding so bad?

Fish food contains various carbohydrates and protein. Uneaten food in the water will be broken down by bacteria in the same way as the fishes waste products. The breakdown of carbohydrates consumes oxygen and produces carbon dioxide, while the breakdown of protein produces ammonia. The combined effects of oxygen depletion and ammonia can be lethal.

Clearly, with better filtration to remove ammonia and oxygenate the water, the risks of killing your fish by overfeeding are lessened. They are not, however, completely eliminated, so you should still take care.

Are air pumps needed for oxygenation?

Oxygen is of course essential for fish. However, it is not always necessary to have an air pump to provide oxygenation. It is a common misconception that water is oxygenated by the bubbles produced by an air pump. In fact, very little oxygen passes from the bubbles into the water.

The main site for gas exchange in an aquarium is at the water surface. A larger surface area clearly provides more area for oxygen to enter the water, but how does filtration or aeration help?

Consider a stream or river: it is well known that fast-flowing waters are well oxygenated, while still, waters are often stagnant. The greater the circulation and surface movement of water in an aquarium, the greater the oxygenation. More oxygen is added when the bubbles from an air pump break the surface than when they rise through an aquarium.

Most filters will provide adequate oxygenation as they circulate the water and cause surface movement. An added air pump will provide even greater oxygenation, and is a good safeguard should the filter ever stop working, but is usually not a necessity.

What is protein skimming?

Protein skimming does not fall into any of the previously defined categories of filtration, but it is a process whereby waste products are removed from the aquarium.

Protein skimming uses fine air bubbles to strip proteinaceous waste products from the water. You may have noticed the white froth that is sometimes formed by waves as they break on the beach. The waves force millions of tiny bubbles into the water and as these rush to the surface, they collect dissolved proteins and the foam results. The same mechanism, although on a smaller scale, is used by protein skimmers in the aquarium. Air, from an air pump or venturi intake, is forced up through a column of water (the reaction chamber), and the foam is collected at the top.

The process of protein skimming can occur in both fresh and saltwater. However, to get protein to foam out of freshwater requires an extremely large reaction chamber and very powerful pumps. Therefore, freshwater protein skimming is not practical for home aquaria.

Protein skimming is however readily achievable in marine aquariums and is commonly used. Because protein skimming removes nitrogenous wastes before they start to decompose, it reduces the production of ammonia and so takes some of the load off the biological filtration. Secondly, it removes nitrogen without producing nitrate. This is particularly desirable in marine reef tanks since nitrate is toxic to corals and many invertebrates.

Protein skimming on its own is usually insufficient filtration, but its addition to marine tanks is beneficial, particularly where invertebrates are to be kept.

Further Reading

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• Cichlid Aquatics: Learn About Haplochromis sp. Fire
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