What is the aquarium’s Nitrogen Cycle?

Although your tank may look crystal clear, do not be fooled. There are toxins dissolved within the aquarium’s water. Sounds scary, but there are hundreds of thousands of bacteria living in your tank who are constantly fighting to keep the water safe for your beloved fish. But what exactly is toxic in the water? Well, mostly ammonia, nitrite and nitrate. Let’s dive straight into the details.

Source of the toxins

It does not matter what kind of aquatic animals you are housing in your tank, in their natural habitat ammonia, nitrite and nitrate will most likely not be a threat on their lives because the concentrations will remain well below lethal. In our aquariums however, it can become a problem if the right precautions are not taken. This is because an aquarium is a closed system where we as the pet keepers control everything.

The main source of nitrogen toxins comes from our fish themselves. Every time a fish goes to the “toilet” it introduces nitrogen pollution into the water by their urine and feces.

Keep in mind that a lot of people see algae eaters, shrimps and snails as cleaner fish but they as well are a source of ammonia of their own.

Furthermore there are often too many fish in the aquarium. This is a problem that we cause ourselves by overstocking the tank. When an aquarium can not handle the waste these fish produce it is a threat for them because the bacteria can not handle the ammonia levels. Make sure not to overstock your tank, and gradually increase the amount of fish in your tank when you are starting an aquarium.

All the fish need food, which we provide for them. It makes sense that we want our fish to not feel hungry, but do not overfeed! When we as fish keepers give them more food than they need and it does not get eaten, it is another source of ammonia that the bacteria in our tank need to deal with.

Ammonia (NH3 )

The first stage of the cycle is ammonia. You might have this in your house already to clean your windows, which is one of the things it is used for. It is a combination of nitrogen and hydrogen, and in gas form is colorless and has a distinctive smell. It can dissolve in water which results in NH3 (un-ionized ammonia) and NH4+ (ionized ammonia) where the un-ionized ammonia is particularly harmful for aquatic animals.

Ammonia is extremely toxic for fish and therefore it needs to be removed from the aquarium. The tolerance depends on the species of the fish, but experiments have shown that the lethal concentration for fish range from 0.2 to 2.0 mg/l. Ideally you want your ammonia to be 0 ppm (parts per million).

Ammonia can be converted to other less harmful substances. This is done by bacteria that are housed in your filter, on the gravel, on ornaments and even on the glass. The bacteria eat up the ammonia and produce nitrite as a result.

Nitrite ( NO2)

Good, now the ammonia is gone but there is nitrite in the water. This is still toxic for your fish but luckily not nearly as toxic as the ammonia we had just a second ago.

If everything in your aquarium is running well, you will never find any nitrite as it is again converted to nitrate (we will get to that in a minute) but it is not impossible to test positive on nitrite. If your aquarium has too much nitrite in it it means that the biological filtration (the bacteria that convert the toxins) is not capable of converting all the nitrite again to nitrate. This can have multiple reason.

  • The aquarium is new and the bacteria colony must still grow
  • Too much waste (overfeeding or too many big fish)
  • Part of your bacterial colony has been destroyed in a large water change

If you have a nitrite problem, make sure you do a rather big (25-30%) water change immediately. This makes sure your nitrite concentration gets diluted. You can improve your biological filtration and make sure your filters are not clogged. These steps will in theory help your fish, but you can move them to a safe and healthy other aquarium if you have one.

Nitrate (NO3 )

The final substance in the nitrogen cycle is called nitrate, and this is the least toxic to your fish. Notice that I did not say that it is not toxic, because nitrate accumulation can be a serious problem.

Plants can help you keep nitrate levels low

When your tank has high levels of nitrate, you can add some fast growing plants like Elodea (often called water weeds) or for example Hygrophila polysperma (I have this in one of my tanks and despite being beautiful it grows like crazy) .

The most natural way to keep your nitrate levels low is a heavily planted tank. All the plants will contribute to low nitrate levels, because they will need fertilizers to grow.


Now you know the essentials of the nitrogen cycle, but I want to give you some tips that help you make sure you keep all the values at a minimum.

Clean your filter
This is a big one, make sure you clean your filter every once in a while. When there are rests of plants, excess food or other organic stuff stuck in your filter, they are out of side but they are most definitely still contributing to the nitrate buildup in your aquarium.

Another cause for ammonia spikes are clogged filters. If there is no water running through the filter the bacteria can not do their job. Recall that there are also bacteria housed in other parts of your tank like gravel, glass and ornaments, but if the water is not flowing the ammonia will obviously also not reach the bacteria.

Do your water changes
When you have been running your aquarium for a long time it sometimes is tempting to only fill up your aquarium to the top to compensate for any evaporation has happened. What you are doing than is neglecting your nitrate build up, as you are not removing any nitrate by diluting it with water changes. This is also called “old tank syndrome“.

Cycle your tank without fish
When you start a new aquarium it is tempting to immediately stock it with fish and other aquatic animals. Please refrain from doing this and instead keep your aquarium running without fish for 2 weeks to a month. This time is needed to grow your bacteria colony that can handle the ammonia that is produced by the fish. If you add fish without a proper colony, the ammonia that the fish produce will not be converted to nitrite and nitrate but will build up instead.

Algae bloom
A sudden increase in algae is a good indicator of an increase in your nitrate levels. Keep this in mind when you notice it in your tank. These are a couple of things you can do to stop the algae from growing.

  • Add fast growing plants that take away the nitrate for the algae
  • Do a water change to remove some nitrate
  • Remove algae that has grown, but make sure you tackled the source first


Banner image – Image owned by Tommy Kronkvist licensed under CC 3.0

Bart Sprenkels

I have been keeping multiple aquariums since I was 18 years old. Just like many of you, I started with two goldfish but quickly learned they were not suitable for aquariums. Later, I switched to a tropical community tank and I also have two pet musk-turtles in a bigger aquarium. You can read more about me here.

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