Biological Pond Filtration

How it works. Biological Filtration

Our ponds are home to far more living organisms than the fish we have stocked and see swimming around ever day. A pond is quite literally alive with micro organisms that have colonised to exploit the food and favourable conditions for their own benefit. These micro organisms (predominantly bacteria) are attracted to the freely available food that is produced by your fish, taking up residence wherever they can find suitable accommodation.

Fortunately for us, these micro organisms digest and breakdown the accumulation of waste that is potentially toxic to our fish in an attempt to maintain balanced environment that will continue to support them (and fortunately support our fish also).

Our ponds will inevitably accumulate nutrients through the food that we feed our koi, and unless these are processed, will lead to water quality problems. How do bacteria work to convert a brand new, sterile pond environment into a balanced ecosystem that literally cleans up after itself?

I find it helpful to think of the processing role that bacteria perform in our pond as a series of complementary processes that carry on where the previous process left off – rather like a conveyored assembly line. The workers are bacteria which can be classified by the job they do or the way they gain their energy.

Heterotrophic Bacteria

Heterotrophic bacteria are like you and me in that they gain their energy from breaking down organic matter. Organic compounds are complex structures such as proteins, carbohydrates, oils as well as other dissolved organic compounds that are either excreted directly by fish or result from the breakdown of other organic substances (such as leaf matter or uneaten food in a settlement chamber). The organic matter that heterotrophic bacteria breakdown is not in itself toxic. However, it’s very presence attracts micro organisms which in turn exert a great demand for oxygen from the pond environment. This could lead to oxygen-deficient conditions that could ultimately stress your koi. The beneficial heterotrophic bacteria use oxygen during respiration and their processing and breakdown of complex organic matter will lead to the release of inorganic by-products which themselves may prove toxic to fish, requiring further processing by a further group of bacteria – called autotrophs.

Autotrophic bacteria

These bacteria gain the energy they require from the transfer of electrons when inorganic compounds are oxidised. If we were autotrophs, we would be able to gain energy from the inorganic elements (such as nitrogen) that we inhale when breathing air. Unfortunately, our heterotrophic nature means that we’re stuck with organic food! Interestingly, the majority of the autotrophic bacteria have been shown to be able to utilise a degree of organic matter from their environment if levels of their preferred nutrients decline.

Autotrophic filter bacteria are aerobic, requiring oxygen to process the different elements. As pondkeepers, on account of it’s potential characteristics, we focus on the processing of nitrogen. But just as important and active in a koi pond are autotrophic bacteria that process other elements such as phosphorous, sulphur and iron.

The steps involved in biological filtration.

Bacteria represent some of the most basic organisms, being only 1 cell in size. Consequently, bacteria do not ingest solid food but secrete specific enzymes externally and absorb the soluble products.

Heterotrophic bacteria secrete a whole range of different enzymes depending on their niche, specialising in a particular group of compounds eg starches, oils etc. Their digestive enzymes break down the insoluble organic compounds (mostly while they are attached to them) absorbing the soluble building blocks that now dissolve into the surrounding water and into the bacteria themselves.


This primary process of breaking complex organic molecules into their component parts is called mineralisation, and is the first step of bacteriological filtration. The mineralisation process produces inorganic nitrogen (usually in the form of ammonia) as this is released when the other non nitrogenous components of the organic substrate are oxidised and used as an energy source. Mineralisation also results in the release of other minerals such as carbon, sulphur and phosphate all of which are cycled further by autotrophic bacteria. We are most concerned with the cycling of nitrogen.


Nitrification is the biochemical oxidation of ammonia to nitrate carried out by aerobic autotrophic bacteria. Ammonia can arise both from the heterotrophic breakdown of organic matter from within the pond, as well as directly from the fish themselves. Fish release the waste nitrogen as ammonia, having utilised other components from proteins for energy. Nitrification is arguably one of the most important natural processes within a pond, as without it, our fish would soon intoxicate themselves. It is carried out in two phases.

Ammonia into nitrite. Although Nitrosomonas is traditionally credited with the conversion of ammonia into nitrite, other genera such as Nitrocystis, Nitrosogloea, and Nitrosococcus also perform this vital role. Their work can be represented as follows:

NH4 + 2OH- + 3O2 = 2H+ + 2NO2- + 4H20

This shows that ammonia is combined with hydroxyl ions (from water) and oxygen to form water, 2 molecules of nitrite and 2 hydrogen ions. These two hydrogen ions interestingly have a downward acidifying pressure on the pond water’s pH showing how important it is to have a buffer in your filter. It also shows how vital it is to have a high dissolved oxygen level in the pond.

Nitrite into nitrate. Nitrobacter and other genera of autotrophic bacteria process the resultant nitrite (which is still toxic) into less toxic nitrates as follows:

NO2- + O2 = 2NO3-

This equation yet again stresses the importance of the free availability of oxygen in the pond. Without it, bacteria are unable to process nitrite. You may have noticed that compared to ammonia, nitrite can prove to be more persistent and difficult to break down in a pond, especially when a filter is maturing. This has been attributed to an abundance of nitrite combining with free hydrogen ions in the water to form nitrous acid as follows:

H+ + NO2- = HNO2

At certain concentrations, nitrous acid has been shown to inhibit the activity of nitrite oxidising bacteria. Consequently, consecutive partial water changes will help to alleviate the high levels of nitrite (and nitrous acid) enabling a filter bacteria to keep on top of the nitrite accumulation.

Other factors that affect biological performance.

Temperature. Fortunately for our ponds, water temperature accelerates the rate of metabolism of bacteria and the breakdown of nitrogenous compounds. Tests have shown that different genera of nitrifying bacteria perform better at different temperatures with some performing better at 20 degrees C and others at 30 degrees C. In this way, an effective coverage of the pond could be achieved by different bacteria becoming more active at different times of the season. One conclusive test showed that no bacterial activity against levels of ammonia and nitrite are detected below 5 degrees C, even over a period of four months.


Oxygen can be a controlling factor and levels should be maintained as high as possible in a pond. Complete inhibition of nitrification occurs at oxygen concentrations less than 1mg/l, with performance tailing off as dissolved oxygen drops towards this level. One of the problems that bacteria have to live with when sourcing their food and oxygen is that it needs to dissolve through a sticky matrix that the bacteria secrete. Successive generations of bacteria will colonise on top of old bacteria ‘skyscraper-style’ until the nutrients and oxygen are no longer able to reach those on the ground floor. These then die, collapse and possibly even lead to the whole tower of bacteria to fall away from the media. This exposes more free surface area on to which new bacteria can colonise. Win this in mind, it makes sense (as some moving biological media already practise), to encourage older and less effective bacterial colonies to leave the media so that new and more active bacteria can colonise the the space, ensuring a faster-growing, more active bacterial colony.

pH. There is strong evidence that nitrifying bacteria can be conditioned to function throughout a fairly wide pH range, provided that they are given sufficient time to adjust to any fluctuations.


Even though the processes of mineralisation and nitrification that are performed by aerobic heterotrophic and autotrophic bacteria respectively detoxify organic and inorganic pollutants, they do not completely remove the compounds from the pond. For example, nitrogen that enters the pond will ultimately be deposited as a relatively safe form of nitrogen; nitrates. These can be removed biologically either by assimilation by plants or by the work of denitrifying bacteria, resulting in the release of nitrogen gas into the atmosphere. The bacteria that perform these final steps of processing have specific environmental requirements which are quite literally the opposite to those of ammonia and nitrite oxidising autotrophs. We design our filters to provide well aerated filter media to accommodate the conditions of ammonia and nitrite oxidising bacteria so it is not surprising to find nitrate levels increase in our ponds; they just do not provide the correct anaerobic conditions for denitrifying bacteria.

Denitrifying bacteria are heterotrophic bacteria that under anaerobic conditions are driven to reduce nitrates into nitrogen gas by removing the oxygen. These bacteria secrete an enzyme called nitrate reductase that releases the oxygen from nitrate that these bacteria require to breakdown an organic food. These bacteria can be encouraged to grow and utilise oxygen by offering them a ready source of soluble organic carbon such as methanol. They utilise the methanol (which is drip-fed into an anaerobic filter), requiring oxygen to do so which they acquire from nitrates under anaerobic conditions; a rare event under typical aerobic pond and filter conditions.

6NO3- + 5CH3OH = 3N2 + 5CO2 + 7H2O + 6OH

Most of us can say from experience that this reaction does not take place in our own ponds as it is typical for us to see nitrate levels accumulate over time. Our best way of overcoming this is to dilute these away with a water change.

In summary, biological filtration comprises a series of complementary bacterial stages that break down and process toxins into a series of less toxic by-products. Biofilters and media are designed and managed so as to enhance the function of these bacteria whose sole objective is to exploit and thrive under these conditions. Fortunately for us and our koi, this also keeps our water ‘sweet’.

Kill blanketweed and string algae.