Fish, Tanks and Ponds

Fish, Tanks and Ponds
A comprehensive guide to fish

Aquarium filtration basics

Torpedo barb, Puntius denisonii
Denisons Barb, Puntius denisonii


Filtration is a vital part of modern fish keeping. In days gone by people tried to emulate nature and use plants in an attempt to make a tank in to a complete eco system which needed no intervention. But to do this successfully is incredibly complicated and unlikely to be achieved in a home aquarium. So we rely on filters to keep the closed environment healthy for the fish we keep.

Types of filtration

Aquarium filtration can be broken down in to three main categories. These are:

  • Biological filtration.
  • Chemical filtration
  • Mechanical filtration

All these types of filtration have an important role to play but by far the most important of the these id biological filtration without which the fish would in most cases die.

Biological filtration

All fish excrete ammonia through their gills, organic waste breaks down in to ammonia.

Ammonia is highly toxic to fish. So all this ammonia has to be dealt with some how. Fortunately there are some micro organisms called bacteria and archaea which have evolved to do this in nature and if we provide them with an ideal environment they will carry out the same role in an aquarium.

The ideal environment for these micro organisms consists of a plentiful supply of oxygen, a solid but wet surface to colonise, a temperature which allows them to be active and minute traces of ammonia and nitrite at immeasurably low levels. All of which are found in the average aquarium filter.

Before this will happen in an aquarium the aquarium has to be matured. This is where bacteria are allowed to colonise the bio-media in the filter. In order for them to be able to do this they must have a source of ammonia available to them which has to be added artificially at first in a process called cycling. Maturing an aquarium takes time and simply leaving the aquarium to stand for a few days prior to adding fish won't achieve anything useful.

Once the aquarium has been cycled and has a good colony of micro organisms present it is deemed safe to add some fish. The fish simply by their presence will add more ammonia to the system which the micro organisms will deal with.

Organic waste such as fish waste, uneaten food, dead fish, dead leaves ect will be consumed by a variety of micro organisms such as bacteria, fungi, protozoa and other single celled organisms in a process called mineralization.

This is usually put in very simple terms where bacteria convert waste in to ammonia and then different bacteria change ammonia in to nitrite and a third group of bacteria change nitrite in to nitrate. But the process is actually quite complex.


Mineralisation is the first stage of decay (often referred to as the nitrogen cycle) and where organic nitrogen is converted in to ammonium (NH4).

The first stage of mineralization is called aminization where large protein molecules are broken down in to amino acids.

The next stage of decay is ammonification where the microbial conversion of organic-nitrogen into ammonia (NH3) or ammonium (NH + 4 ) occurs. Once all the organic nitrogen has been converted in to ammonia and ammonium all else that remains is biologically and chemically inert dust like material called mulm.


Depending upon the pH and temperature most ammonia will be in the form of ammonium (NH4). The oxidation of ammonium in to hydroxylamine is the next stage of decay. This process obviously requires a lot of free oxygen without which the process will not occur.

2NH4 + O2 → 2NH2OH + 2H
(ammonium + oxygen becomes hydroxylamine + hydrogen gas).

The second stage of nitrification where the hydroxylamine becomes nitrite is as follows.

2NH2OH + 2O2 → 2H + 2H2O + 2NO2
(hydroxylamine + oxygen becomes hydrogen gas + water + nitrite). Again this process requires a lot of free oxygen or it will be inhibited.

Both ammonia and nitrite are very toxic to the fish and so no fish should ever be subjected to elevated levels of either compound.

The next stage of nitrification is where the nitrite (NO2) is oxidised further and becomes nitrate (NO3).

2NO2 + O2 → 2NO3
Nitrite + oxygen = nitrate.

Nitrate is relatively non-toxic at low levels but if it is allowed to rise to high it will have a negative impact on the fishes health.

In most aquaria this is the end of the process of biological filtration. Nitrates continue to build up in the water and are generally removed by making regular partial water changes using nitrate free water.

All biological filters have to run all the time, night and day. It is extremely important that they are never switched off or the bacterial colony will be damaged and the water quality will suffer greatly as a result.

Chemical filtration:

Chemical filtration allows the removal of dissolved compounds which might otherwise pollute the water of an aquarium. Any media which alters the chemical make up of the water falls in to this category. The most popular and most widely used chemical media is of course carbon. Carbon filters are most effective at removing chlorine, and volatile organic compounds (VOCs) from water. They are not effective at removing minerals, salts, and dissolved inorganic compounds. It will remove any colour from the water, but it will also remove some of the active ingredients from medication. It won't make any difference to the nitrate level and some cheap carbons will actually increase the phosphate level. Contrary to popular opinion carbon will not release pollutants back in to the water if it is left in the aquarium for to long.

Biomarine poly filters will remove a long list of contaminants including ammonia and nitrite. Water softeners will remove the hardness from water but if they are the type which are recharged using salt then the calcium and magnesium will be replaced with sodium so the level of dissolved solids will remain relatively high.

Nitrate removal resins which are recharged using salt will replace the nitrate with chlorides so again this isn't an ideal way of dealing with nitrates. Chemical filtration has a role to play but if a good regime of partial water changes is adhered to it is arguably the least important type of filtration in most aquaria. Unlike biological media, all chemical filtration media need replacing on a regular basis if it is to remain effective.

Mechanical filtration

Mechanical filtration refers to the filtration which removes solids from the water column. This is desirable in an aquarium so that the fish can be enjoyed by seeing them at their best in clear water. Mechanical filtration is only important from an a aesthetic point of view. Mechanical filtration media also needs to be changed regularly or it becomes blocked up with sediment. Once this happens the flow rate of the filter will be slowed and this could impact on the biological filtration. To prolong the life of the mechanical filtration media use different grades starting with the most coarse media first followed by a medium grade and finally a fine media last of all.

Types of filters

External power filter

Probably the best option for most fresh water aquariums. External power filters are extremely versatile and can be used for combination filtration where all three types of filtration mentioned can be used alongside each other in a single unit. As their name suggests an external power filter sits outside the aquarium so there is very little to have to conceal with in the tank. Some external power filters even combine an heater and thermostat within them. In the event of a failure they cannot pollute the water in the tank and maintenance is easy because they are so accessible.

Internal power filter

Internal power filters are quite similar to the external power filter but generally have smaller canisters and so offer less options for the types of filtration although they are still able to offer a combination of all three type of filtration with careful planning. They have the disadvantage f being difficult to conceal while remaining accessible for maintenance and are more suited to the smaller to medium sized aquarium.

Under gravel filter

Under gravel filters are extremely efficient biological filters. They are only capable of biological filtration and they require a lot of maintenance to keep them running at their peak performance. Because water is passed through the substrate which becomes an active bio media it also acts inadvertently as a mechanical filtration media and it can very quickly become blocked up. To avoid this the substrate needs to be sifted and stirred up on a regular basis and all the debris siphoned away. As with the external power filter there is very little to conceal with an under gravel filter. One big disadvantage with these filters is that plant growth is generally very poor when one is in use.

Air operated sponge filter

This is a specialist filter normally used in breeding tanks. They are one of the safest filters to use with very young fry because there is no risk of the fry being sucked in to the filter or becoming trapped on the strainer. A sponge filter carries out both mechanical and the all important biological filtration once it has been matured. Don't try to keep a sponge filter spotlessly clean, as long as there is a good flow of water through it then it will work.

Sponge filters which are maintained properly develop a bio film on their surface, this is made up of all manner of micro organisms and algae and very small fry are able to graze on it and by doing so meet most of their early food requirements.

Other filtration devices

Protein skimmer

Going back to the biological filtration part of this article you will recall that the first part of decay is called mineralization. Where microbes break down organic nitrogen in to proteins before going on to the nitrification process which ends up at nitrate. A protein skimmer is able to make use of the fact that proteins are large molecules which are hydroscopic at one end and hydrophobic at the other end which means in simple terms that one end is attracted to water and the other end is repelled by water. A protein skimmer passes millions of very fine bubbles through a column of water which is traveling in the opposite direction to the bubbles. The protein molecules stick to the bubbles at the end which is hydrophobic while the other end remains in the water. When these bubbles reach the surface they form a fairly stable foam which is collected in a collection cup which sits on top of the protein skimmer.

The advantage of using a protein skimmer is that most of the waste which would go on to form nitrate is actually removed before nitrification takes place.

Due to the physical properties of fresh and salt water, protein skimmers are only really efficient in marine aquaria and don't really work in fresh water due to the difference in the size of the bubbles which are able to form in the two environments.

Chemical filter media


Carbon will remove lots of different chemicals and compounds from water with varying degrees of success. It is very good at removing:

  • Organic compounds
    • Pesticides
    • Herbicides
  • Chlorine
  • Medication
  • Tannins
  • Urea

Carbon shouldn't be relied upon to remove the following because although it will remove small amounts it is generally ineffective at  removing:

  • Heavy metals
  • Minerals and salts
  • Hydrogen sulphide

Carbon will not remove:

  • Ammonia
  • Nitrite
  • Nitrate
  • Phosphate

Some cheap carbons can actually add to the phosphate level in the aquarium.

Carbon will NOT release chemicals and/or compounds back in to the water once it has reached the end of its useful life.

Old spent carbon can be left in the filter where it makes a superb bio media for useful bacteria to colonise.


Zeolite is marketed as an ammonia remover which it does along with other nitrogenous compounds.

Zeolite is also an effective water softener and if used in hard water it will become saturated with calcium before having much effect on ammonia.

It should also be noted that if zeolite is used as a water softener the calcium is replaced with sodium so while the water will be softer the total dissolved solids will not alter significantly.

BioMarine Polyfilter

Polyfilters will remove:

  • amino acids
  • proteins
  • lipoproteins
  • dissolved organic matter
  • all forms of phosphates
  • tannins & humic acids and related complexes
  • volatile organic chemical such as chloroform
  • bromoform
  • benzene
  • phenols
  • organophosphate
  • insecticides/pesticides
  • All metabolic wastes

Polyfilters will not have a significant effect on nitrate.

Polyfilters although quite expensive are well worth keeping in stock in case of an emergency unknown water quality issue where they can be absolute life savers for your fish as well as buying you some valuable time.


Living article/193977

Poly Bio Marine Inc