One way to learn about water chemistry and artificially create an aquatic ecosystem is to build an aquarium. Aquariums are amazing ways to enjoy beautiful fish and plants from many different aquatic ecosystems. 

But aquariums can not simply be started with dechlorinated water and adding fish or plants. There is a very important set of chemical reactions happening that you must understand to set up and maintain an aquarium. 

Please research Cycling and some of the basic chemical terms below before planning an aquarium. 

Planted Cycling

The basics of cycling are covered in a separate article. This article discusses aspects of the nitrogen cycle in more detail. 


Aerobic Bacteria
This is bacteria that requires oxygen to live.

Anaerobic Bacteria
This is bacteria that can live without the presence of oxygen, or bacteria that does not require oxygen.

This chemical is the result of fish waste and decomposing food in the aquarium. Ammonia is the leading killer of tropical fish. New tanks that are going through the aquarium cycle or heavily stocked tanks will show ammonia readings with your test kits. Ideally, we want the ammonia reading to be 0 ppm.

The ammonia level should always be zero (that is, undetectable by conventional test kits) in a mature aquarium. Fish waste, uneaten food and decaying plant matter will all contribute to the level of ammonia in the tank. However, in a mature tank, there are usually enough ammonia-converting bacteria to ensure that it never rises to detectable levels. However, there are situations which may result in a temporary rise in ammonia levels, even in a mature tank. These include:

  • Filter failure, or lack of maintenance
  • Use of medications
  • The addition of a large number of fish at the same time
  • Over-feeding
  • Over-enthusiastic cleaning of 'biological' filter media.
In such circumstances, the bacterial population will need time to increase or recover to cope with the demand. If fish appear unwell, testing for the presence of ammonia should be a priority.

The total ammonia in an aquarium will be present in two forms: ammonia (NH3) and the ammonium ion (NH4+). The proportion will depend mainly on pH, and to a lesser extent temperature. At alkaline pH, more of the ammonia will be present as the more toxic NH3, while at acidic pH, more of the less toxic ammonium (NH4) will be present. Ammonia poisoning is therefore more common at alkaline pH.

Ammonia can cause damage at levels of only 0.1 ppm (which is below the level detected by many kits!). There may be haemorrhaging and destruction of mucus membranes, the gills are particularly likely to be damaged, and may appear reddened. As with nitrite poisoning, fish may apppear to gasp for air at the surface, and show rapid gill movement. Higher levels, of several ppm, can be fatal.

In a mature aquarium, ammonia is oxidised by bacteria to form nitrites. The chemical reaction which occurs is shown below:

+ 2 H2O
>>> NO2-
+ 8 H+
(hydrogen ions)

For many years the bacteria responsible were thought to be Nitrasomonas species, but more recent research indicates that these bacteria may do little or nothing in freshwater aquaria, and that bacteria known as Nitrosococcus may be the true ammonia-oxidisers in our aquaria.

Chloramine is a combination of chlorine and ammonia. It is a stronger disinfectant than chlorine alone and is used in areas where this extra disinfectant is needed. As with chlorine, you must eliminate this chemical from your tap water before adding it to your aquarium or it too will kill your tropical fish.

This chemical is found in most tap water and it is used to kill the bad bacteria in our drinking water. Clorine must be eliminated before entering your aquarium or it will kill your tropical fish.

This heavy metal can come in with the tap water if you have older copper pipes. It can also get introduced to your tank if you've used any copper based medications. Copper can be very harmful to fish and invertebrates.

 Dissolved Oxygen

Oxygen is as critical to fish life as it is to human life. DO refers to the oxygen gas that is dissolved in water. Fish absorb the DO directly from the water into their bloodstream through their gills. Although some species, such as bettas and gouramis, are capable of breathing air, sufficient oxygen levels should always be maintained in the water for all fish.

The amount of oxygen water can hold (saturation) is dependent upon water temperature, salinity and atmospheric pressure. As water temperature increases, the amount of oxygen the water can hold decreases. Likewise, as salinity increases, less oxygen can be dissolved into the water. At greater pressures, water can hold more oxygen. For example, more oxygen can be held in water (of equal temperature and salinity) in Miami than at the much higher altitudes of Denver.

Nitrites are converted to nitrates during the cycling process. Nitrates are not as toxic as ammonia or nitrites but they are harmful and will stress your fish at high enough levels. The only way to remove the nitrates is through a partial water change. Ideally you want to have test kit readings of less than 20 ppm in freshwater tanks and even less in saltwater tanks.

In the past, nitrate was considered essentially harmless to fish; certainly it is far less toxic than ammonia or nitrite. It has been shown that levels of up to 1000 ppm may be required to cause death, but the effects of lower levels on long term health are not well understood. The sensitivity of different species to nitrate levels varies, and there may be long term effects on general health, growth and breeding ability.

Generally, many aquarists seem to agree that keeping nitrates below 50 ppm is necessary to prevent any long-term effects on fish health, but below 25 ppm is more desirable. Remember that many fish may come from a natural environment where there is little or no detectable nitrate. Fish which have been aquarium bred for generations are more likely to tolerate nitrates.

Ammonia gets converted to nitrite by the bacteria in your tank. Nitrite levels will soar in new tanks that have not yet been cycled. Nitrite is just as toxic to tropical fish as ammonia and the only way to quickly reduce nitrite levels is through a water change. Nitrites will eventually be converted to nitrate by the bacteria growing in the tank and filters. Ideally, in established tanks you want this reading to be 0 ppm with your aquarium test kit.

The nitrite level should always be zero in a mature tank. A temporary rise in nitrite levels may be seen for the same reasons as listed for ammonia above. However, the nitrite spike may persist longer, so if there is a delay in testing after a problem has occurred, it is more likely that nitrite will be detected. A nitrite level of only 0.1 ppm could prove harmful if exposure is prolonged. Symptoms of nitrite poisoning include gasping and rapid gill movements, which could be mistaken for a shortage of oxygen. In extreme cases, fish can actually die of suffocation because nitrite binds to the oxygen-carrying component (haemoglobin) in the blood.

In a mature aquarium, nitrite is oxidised by bacteria to form nitrate. The chemical reaction which occurs is shown below:

+ H2O
>>> NO3-
+ 2 H+
(hydrogen ions)

It was originally thought to be Nitrobacter species which were responsible for nitrite conversion to nitrate in aquaria, but again, recent research (by Dr. Timothy Hovanec and others) indicates a different group of bacteria - Nitrospira - are responsible.

Nitrogen Cycle
This cycle usually takes from 2-8 weeks to complete and will happen in all new aquariums. You could speed up the process by using the filter material or gravel from an established tank. Even then it could still take a few weeks for the tank to cycle. This is the cycle whereby Ammonia is converted to Nitrites and Nitrites are converted to Nitrates. Please read the Aquarium Nitrogen Cycle article for more information.

Ammonia   ->   Nitrite   ->   Nitrate

pH is the scale used to measure the acidity or alkalinity of water. The scale ranges from 0 to 14 with 0 being the most acidic, 7 being neutral and 14 being the most alkaline. It is possible to raise or lower your pH levels with water changes or chemicals from your local pet store.

Phosphate can be introduced to your aquarium mainly from tap water, dead plants and fish food. High phosphate levels can cause algae outbreaks. There are products on the market to remove phosphates and you can do your part by keeping up with your aquarium maintenance and performing regular water changes. Saltwater reef tank keepers and freshwater plant keepers may want to invest in a phosphate test kit.

This is the amount of dissolved salts in water and is measured using a hydrometer.

Specific Gravity
This is a density measurement for the amount of dissolved salts in saltwater compared to freshwater. Explained another way, saltwater is composed of many more elements than freshwater. The specific gravity measurement shows us how much heavier or denser saltwater is compared to freshwater.

Water Hardness
The hardness level of water has to do with the amount of minerals that are dissolved in the water. Calcium and magnesium are the primary minerals that are dissolved in tap water. "Soft" water has relatively few dissolved minerals whereas "hard" water has many dissolved minerals. Water hardness is not really an issue unless your water is excessively soft. Then you may have problems with runaway pH levels. For saltwater aquariums this is especially true. The carbonate hardness of saltwater can give you a good indication of how stable your pH is.

Fishless cycling

This is a method which uses pure ammonia to start the nitrogen cycle in a new aquarium, rather than the wastes of a few unlucky fish! The method was popularised by Dr. Chris Cow.

Essentially, the ammonia solution is added to the aquarium daily. When the ammonia-converting bacteria have established, the ammonia reading should fall back to zero overnight. The addition of ammonia is continued at a reduced level to keep the process going as nitrites rise and then subsequently fall as the nitrite-converting bacteria become established. When nitrites read zero, the tank is cycled and a water change is carried out to reduce any resulting nitrate before fish are added.
The advantages of this method are obvious - no fish are exposed to the toxic waste products during the cycling process. It also means the aquarium can be stocked with more fish straight away, as there is a full compliment of bacteria established. The fish wastes essentially take the place of the ammonia additions.

More details on fishless cycling can be found in Dr. Chris Cow's article

An example of an actual Fishless Cycle can be found here.