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The Nitrogen Cycle and Your Aquarium

Dec 7, 2007
When fishes, plants, and food are introduced into the aquarium a process known as nitrification occurs, this is referred to as the nitrogen cycle. This is not unique to aquaria; nitrification will occur in any body of water, or soil, where bacterial action breaks down decaying organic matter and converts it into ammonia. Ammonia compounds are then oxidized into nitrite and nitrates.

These nitrifying bacteria can be termed as beneficial or friendly bacteria, without them aquarium inhabitants could not survive. The process begins with Heterotrophic bacteria consuming fish waste, decaying vegetation, and uneaten food, and converting them into ammonia.


Ammonia (NH3) is a colourless, pungent, suffocating gas, a compound of nitrogen and hydrogen, and is very soluble in water. The majority of waste produced by fishes is in the form of ammonia, most of which is secreted through the gills. The remainder excreted as faecal matter, is converted to ammonia by Heterotrophic bacteria.

Ammonia is extremely toxic to fishes and must be removed or broken down. Visual signs of fishes succumbing to this toxicity include:

Gasping at the surface
Cloudy eyes
Frayed fins
Listless behaviour
Increased mucous production
Possible internal and external bleeding (if extreme toxicity exists)

Because of the toxic effects of high levels of ammonia there maybe fatalities, even after ammonia levels are brought under control. Smaller fishes have a higher gill surface area relative to larger fishes; and are therefore more susceptible to ammonia toxicity.

Water changes are the best way to solve ammonia problems. You should do partial water changes over a few days, to bring levels down. Resin-based media or Zeolites are available at aquatic shops and are very useful at removing various substances from fresh water aquariums, including ammonia. Moving fishes to a safe tank will stop the absorption of ammonia immediately, and they can be returned to the main tank when ammonia levels return to zero.

If you have a high pH level, you could try reducing it to nearer 7.0, as this will also reduce the ammonia toxicity.

pH is an important factor in controlling many chemical balances, of which ammonia and ammonium are included. pH is logarithmic, and this is the controlling factor over the presence of ammonia or ammonium. Ammonium (NH4) is less toxic than ammonia, and is formed when ammonia reacts with acids, therefore, if ammonia is present in the aquarium, and the pH of the water is acidic, then ammonia will become ammonium.

As pH rises, so does the toxicity of ammonia, i.e. a pH increase from 7.0 to 8.0 would be a ten-fold increase in the hydroxyl ion, (and decrease in hydrogen concentration) and ultimately a ten-fold increase in ammonia toxicity. It is therefore necessary to test for ammonia before significantly increasing pH.


Ammonia testing will show a zero reading when the nitrogen cycle is working well, and the Nitrosomonas bacteria are consuming the ammonia and converting it into nitrite. Nitrite (NO2) is also toxic to fishes if it is not removed or converted during the nitrogen cycle into nitrates.

Levels above 1ppm need to be removed by carrying out substantial water changes. This should be done on a daily basis for a number of days, testing regularly, until the nitrite level has reduced to zero. Moving fishes to a safe tank will stop the absorption of nitrites immediately. They can then be returned to your main tank when nitrite readings show zero. Symptoms of nitrite toxicity include:

Gasping at the surface
Blood and gills turning brown

Nitrite is also dependent on pH, and if pH drops below 6.5, when nitrite is present in the water, the nitrite will convert to nitrous acid. This too, is very toxic to fishes.


Nitrate (NO3) is the end product of the nitrogen cycle, and is relatively non-toxic; although in high concentrations can still be a problem. Nitrite is converted into nitrate by the bacteria Nitrobacter, and the presence of nitrates in a freshwater aquarium indicates that the nitrification process is working.

Some species are more tolerant than others to nitrate, but a sensible approach would be to keep levels below 50ppm (mg/l). Some of the symptoms of nitrate toxicity would be:

General poor health
Poor growth
Poor colouring
Less tolerance to disease

Nitrates are an essential food source for plants and algae, so if you encourage healthy plant growth in your aquarium, levels will be reduced. Otherwise, if tests show high levels, it would indicate a partial water change is necessary. Regular partial water changes when carried out during maintenance will usually keep it under control anyway.

Ammonia and Nitrite levels will tend to be at their highest in the first 4 to 6 weeks of establishing a new aquarium. This is usually known as new tank syndrome.

Hydrogen Sulphide (H2S) is an extremely poisonous gas that smells like rotten eggs, even in small concentrations it can cause a quick death. It is produced during the decay of organic matter that contains sulphur, and by the action of dilute acid on the sulphides (acid aquariums being at risk).

The usual cause in the aquarium is probably one of neglect, by not keeping the substrate clean of dirt and debris, thereby allowing the decay to build up. An early indication of this problem can be a sudden bloom of algae. The poisonous gas affects fishes by binding the iron of the bloods haemoglobin, which blocks the absorption of oxygen; this causes symptoms, which include:

Respiratory problems
Gasping at surface
Unusual colouration of the gills

Regular aquarium maintenance, being sure to clean all debris from the substrate, will prevent the problem arising.
About the Author
For more information about freshwater tropical fishkeeping please visit my site at www.freshwatertropicalfishkeeping.com for 30 years or more of fishkeeping experience. Or watch out for more fishkeeping articles from me, Kevin Yates at FWTFK
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