Nitrogen Cycle In Aquariums: A Simple Guide For Beginners

Unlike the natural habitats of most tropical fish species, where dangerous levels of nitrogen-containing compounds are rare, the home freshwater aquarium is a closed environment in which overpopulation and overfeeding are common. That makes your fish tank ripe for excess ammonia and nitrification in the water, which is the most common cause of illness, disease, and even death in aquarium fish.

In this guide, we explain how the nitrogen cycle works in the aquarium, as well as give you lots of helpful tips on how to keep your tank water pristine and safe for your fish.


In nature, the nitrogen cycle describes the process in which nitrogen passes from the air to plants, from animals to bacteria, and then back to the air. That system works fine and does not need human intervention. However, the cycle works differently in the closed environment of the aquarium.

In a fish tank, the process is a biochemical mechanism that sees the continual degradation of various nitrogenous compounds, from ammonia to nitrite and nitrate. In the last phase of the cycle, the nitrates are taken up by the live plants in the tank and used as nutrients or removed from the water by partial water changes and your biological filtration system.


In the aquarium, it is up to the aquarist to manage the nitrogen cycle effectively through the use of a biological filtration system. The biological filtration system contains sponges that act as a platform for the growth of beneficial bacteria. Those bacteria are vital to the nitrogen cycle process as they work to break down ammonia and nitrites produced by fish waste and decaying organic matter, keeping the water safe for your livestock.

It takes up to three months for a colony of bacteria in the filter system to become established enough to convert ammonia and nitrites to nitrate. For that reason, it is wise to take some time to stock a new aquarium with a few small fish at a time to allow the biofilter to keep pace with the gradually increasing bioload in the tank.


The nitrogen cycle is the process by which certain bacteria process harmful waste. There are three stages in the cycle:


The first stage of the nitrogen cycle is the decomposition of organic matter, such as uneaten food, dead plant leaves, dead organisms, and waste produced by fish and invertebrates. As bacteria break down these materials, protein metabolism produces ammonia.

Ammonia is a colorless gas that is extremely toxic to fish, and even low levels in the water will cause oxygen starvation and even burn delicate fish gills. High ammonia levels in aquarium water usually occur because there are too many fish in the tank or because the fish are overfed.


In a balanced aquarium, nitrogen-fixing bacteria called Nitrosomonas consume the ammonia and oxidize it to create nitrite. Nitrite is also toxic and impairs the oxygen-carrying capacity of the blood, but fish can generally handle twice as much nitrite in the water as ammonia.


In the third stage of the nitrogen cycle, bacteria called Nitrobacter process nitrites and release a less toxic chemical called nitrate. Although nitrates are not toxic at low levels, if the concentration exceeds 20 ppm, they can become dangerous to fish. In nature, nitrate is converted aerobically to harmless nitrogen gas. That doesn’t happen in the closed environment setting of most aquariums, which means partial water changes are necessary to dilute the nitrate.

Live plants help remove nitrates from the water in freshwater tanks. In a saltwater setting, live rocks and deep sand beds can provide anaerobic areas where denitrifying bacteria process nitrates into nitrogen gas, which then harmlessly evaporates.

This diagram of the aquarium nitrogen cycle illustrates the process perfectly.


So you can see that the key to clean, healthy water that is free of toxins and safe for your fish is to get the nitrogen cycle established and working efficiently. The process of establishing and maturing your biological filtration system is known in the hobby as «cycling.»

In a new tank, you can cycle the aquarium with or without fish.


When you add fish to your new aquarium, they begin to produce waste and ammonia, and decomposing fish food will also be added to the mix. Unfortunately, these fish often don’t survive, earning them the nickname «suicide fish.»

Since a new filtration system does not contain colonies of Nitrosomonas bacteria established to consume the ammonia produced by the fish, levels of the toxin rise and eventually rise until the bacteria population catches up.

You can see that phenomenon happening quite easily as the aquarium water temporarily turns cloudy. Once the bacteria take control of the situation by breaking down the ammonia, the water will become clear and the ammonia level will drop.

nitrite tip

As the Nitrosomonas bacteria consume the ammonia in the tank, nitrite is produced. As the number of bacteria increases, the level of nitrite also increases. In response, the population of nitrite-eating Nitrobacter bacteria skyrockets due to the amount of nutrients that are available to them.

Once that nitrite peak is reached, the nitrite levels in the water will drop, as bacteria break down the chemical faster than it is being produced.

Nitrate Management

The end product of the nitrogen cycle is nitrate. While in low concentrations in the water, nitrate is not as dangerous to fish as ammonia or nitrites, although it can cause other problems in the tank, such as algae blooms.

To control the levels of nitrates in the water, it is necessary to carry out partial water changes every week. The addition of live plants is also extremely effective at controlling nitrate, as the plants draw the chemical from the growing medium and water column to use as a nutrient-rich fertilizer.

When does the aquarium «cycle»?

The usual method of cycling a new tank is to introduce some hardy fish to start the nitrogen cycle. The idea of ​​using these starter fish is to introduce ammonia, fish waste, and food into the mix. Once your test kit no longer registers ammonia and nitrite levels in the water, the cycle is complete.

How long is cycling?

In a tank where there are fish, the tank cycle can take 30-45 days. Once the cycle is complete, you can add more fish to your community, as the bacteria colonies in the filter media can now cope with the additional bioload.


If you don’t want to risk the lives of your new fish by placing them in an unrecycled tank, you may prefer to cycle the tank without fish. There are two ways to do it.

Use fish food to cycle the tank

Start by setting up your new tank with everything you need except fish, including:

  • Filtration
  • Heater
  • Turning on
  • Protein skimmer for marine and reef setups
  • Floors

Set your heater to around 82° Fahrenheit, turn on the filter pump and start “feeding” the tank with fish flakes.

As the food breaks down, it releases ammonia, which causes the aquarium to begin the cycling process.You can speed up the process by seeding the tank with a small amount of substrate, filter media, decorations, etc. of an established tank. These items introduce bacteria to the new aquarium, and the ammonia produced by the decaying fish food will provide enough nutrition for the new colonies to establish and expand.

Essentially, the nitrogen cycle works the same way as described above; ammonia converts to nitrite and nitrite then converts to nitrate.

Disadvantages of cycling without fish

The fishless method of cycling the tank has some drawbacks. First of all, the ammonia produced by the decomposition of the fish food may not create enough colonies of bacteria to deal with the fish when you introduce them. So there is still a danger that the arrival of the fish will cause spikes in ammonia and nitrate.

However, these new spikes are usually shorter and less intense than those that occur during the initial cycle. Therefore, the fish are much less likely to suffer ill effects and consequently the survival rate is higher.

Cycling a tank using ammonia

Whether you take the fish or fishless route to cycling your tank, both methods have one thing in common; ammonia.

Did you know that you can use pure ammonia to cycle your aquarium? Well, you can, and introducing pure ammonia into a tank without fish is a very effective method of starting the cycling process.

Simply add five drops of pure ammonia per ten gallons of water every day. Ammonia levels in the water will quickly rise from zero to 5 ppm and higher. Continue to test the water daily, and once nitrites can be measured, reduce ammonia to just three drops per day. Continue adding ammonia until the ammonia and nitrite measurements are zero ppm, which means the aquarium is fully cycled.

Important points to note

When setting up your tank for cycling without fish, you want to make sure the water is well-oxygenated. That’s because the bacteria in the filtration system need oxygen, so it’s helpful to add plants to the setup and perhaps include an air stone as well.

Make sure that the ammonia you use does not contain any additives or perfumes. Also, do not treat tank water with any conditioning product known to remove ammonia. When the cycle is complete, put some activated carbon in the filtration system to get rid of any possible perfumes or additives that may have been hidden in the ammonia you used.

Finally, once you introduce the fish to the aquarium, they will produce enough waste to maintain the cycle and balance the environment within their habitat and therefore you can stop stocking the tank with ammonia.


Before you start cycling your aquarium, whatever method you decide to use, you will need to invest in several test kits that you will use to check the levels of ammonia, nitrite, and nitrate in the water.

Throughout the cycling process, you will need to test your tank water every day to get an idea of ​​where you are in the cycling process. Here are some helpful links to test kits we recommend:

  • ammonia test kit
  • Nitrite test kit
  • Nitrate test kit
  • Salt water test kit

Be sure to carefully read and follow the test kit manufacturer’s instructions so that your test results are accurate. Remember that you are aiming for zero ammonia and nitrite levels and a maximum nitrate level of 20 ppm.


Typically, a tank cycle takes between two and six weeks, although that length of time varies, depending on a number of factors, including:

  • the level of ammonia that is present during the cycle period
  • the efficiency of your biological filtration system
  • if you have used live plants or live rocks in the process
  • if you have used any type of enhancing additives or biomedia

If you decide to go the route of cycling your tank with fish, you can expect it to take up to six weeks for the cycle to fully establish itself and function efficiently.

A big advantage of using ammonia to cycle your aquarium is that the entire cycle can be completed in just seven days, and the scenario is similar if you use the stocking method described above. Also, once the tank is cycled, the bacteria colonies present are large enough to cope with a fully stocked aquarium.


Waiting for your aquarium to turn on before you can add fish is frustrating, but there are a few ways to speed up the process:


Add filter media, substrate, or rocks from an established aquarium. That is the most effective way to speed up the nitrogen cycle in a new tank. Period.

Adding filter media from a cycled tank initiates the bacteria population in the new environment, helping prevent ammonia and nitrite spikes, and shaves weeks off the usual nitrogen cycle timeline.

However, you should make sure the established aquarium is healthy and free of signs of disease or parasites before adding anything to your new tank.


Bacteria in the nitrogen cycle reproduce more quickly in a warm environment and increasing water temperature helps increase the bacteria population rapidly. From personal experience, the sweet spot for maximum bacteria growth is between 82° and 87° Fahrenheit.

That temperature is fine when cycling with an empty tank, but it is too high for many species of fish and could be harmful to them.


Like fish, bacteria that consume ammonia and nitrite need well-oxygenated water to thrive. So by increasing the oxygen saturation levels in the aquarium you can really boost bacterial growth. Also, warm water is not efficient at holding oxygen, so increasing levels through the use of an air stone is a good plan if you intend to increase the temperature of the tank as well.


Nitrifying bacteria grow faster in a darker environment. Therefore, keep your tank lights off until the cycle is complete. Also, don’t allow too much natural sunlight to illuminate the aquarium, as that inhibits the growth of bacteria and causes algae to bloom.


Nitrifying bacteria grow best in an environment where there is a constant flow of water, no lighting and a porous surface. Therefore, allowing your filtration system to run during the cycling process can greatly increase bacterial growth.


If the pH level of the water drops below 7, the growth of bacteria in the tank can slow down or stop altogether. So be sure to test the pH regularly and increase the level if it drops below 7.


Whenever you add tap water to the tank, always use a dechlorinator to remove chlorine and chloramines from the water. These chemicals are deadly to the bacteria you are trying to grow in your tank and are also toxic to your fish.


Ammonia-eating bacteria live on the surface of plant leaves, so adding a few plants from an already cycled tank is a great way to speed up the nitrogen cycle. However, remember to check the leaves carefully for snails before introducing them to your new setup.


Another way to speed up the aquarium cycling process is by adding live, concentrated nitrifying bacteria from a bottle. That sounds great at first, but results tend to vary, largely because not all of these products contain the same species of bacteria.

Although all types of nitrifying bacteria are capable of consuming ammonia and nitrites, not all bottled bacteria products contain those specific types of bacteria that will grow in your filter media. One product that definitely contains those essential bacteria is Tetra SafeStart.

When used according to the manufacturer’s instructions, the bacteria in a bottle can significantly increase the rate of cycling your tank. However, you must store the bottle properly, i.e. away from direct sunlight, excessive heat and cold, or the bacteria may die. Also, once the bottle is past its expiration date, the bacteria inside are most likely dead or dying and of no use to your aquarium’s cycling process.


It is true that you never stop learning when you have fish. But here are some important tips for a healthy new aquarium to help you get off to a good start.


First, and most importantly, you must cycle your tank properly, using one of the methods we’ve outlined above. A properly cycled tank will be safe for your fish and help you get off to the best possible start.


In order for your fish to stay healthy, the water in your tank must be clean and free of toxic chemicals.

I highly recommend that you get into the habit of testing your aquarium water at least once a week to monitor the levels of ammonia, nitrite, and nitrate in the tank. You should also check the pH level of the water to make sure it is suitable for your fish. If necessary, you may need to add a pH buffering chemical to the water to correct the hardness of the water.


Get into the habit of doing partial water changes every week to remove excess nitrates from the water. Also, lighten the load on your filter by removing fish debris and substrate debris with an aquarium vacuum. Try to change up to 30% of the tank water and remember to add dechlorinator to the tap water before adding it to the aquarium.


Over time, filters can become clogged with general dirt and debris. So about every month, remove the tank filter and rinse the unit in a bucket of tank water. You can also use a soft old toothbrush to clean the impeller so it can move freely.


One mistake novice aquarists often make is overfeeding their fish. Uneaten food ends up as waste in the substrate, which then breaks down and contaminates the water. Also, many species of fish can suffer from serious health problems if they eat too much, so feed your fish friends little and often.


Did you like our guide on the nitrogen cycle in the aquarium? I hope you found the information helpful and that you now understand the importance of cycling your new tank before rushing out and stocking it with fish.

Key takeaways…

Certain species of bacteria consume the harmful ammonia produced by fish and decomposing waste, converting the ammonia to nitrite and ultimately relatively harmless nitrates that are removed by plants and regular water changes. Cycling your tank involves allowing those bacteria to take up residence in your filtration system, purifying the water, and making the environment safe to welcome your new fish.

Tell us what you thought of this guide in the comment box below and share the article with other hobbyists if you liked the guide and found it useful.

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