All that a Beginner Needs to Know About the Nitrogen Cycle


When researching how to properly take care of your aquarium, you might come across something called the Aquarium Nitrogen Cycle. This may at first seem like a daunting subject, with lots of chemical terms. I felt the same, but did the research and now can take way better care of my fish. I urge you not to worry and instead read the following article where I take you through the Aquarium Nitrogen Cycle and teach you step by step how to take better care of your aquatic pets!

What is the aquarium nitrogen cycle? The nitrogen cycle is the process that happens inside your aquarium from toxic ammonia, to less toxic nitrite, to nitrate (safe if moderate concentration). This is done by a colony of beneficial bacteria that live mostly in your filter and gravel.

The nitrogen cycle is complex but crucial to know when you are starting and keeping an aquarium. When you master all aspects you can take way better care of your fish and potentially even prevent them from dying. I will explain everything to you in the rest of the article. 

Processes of the Nitrogen Cycle

After a fish releases waste, parts of this waste turns into ammonia, ammonia is a very toxic chemical found in both urine and cleaning products. 

Ammonia can be deadly for your fish in quite small doses so it is important to take care of removing ammonia from your aquarium as soon as possible, but fear not, help arrives in the form of two different groups of beneficial bacteria! So lets get technical and a bit scientific!

Beneficial bacteria called Nitrosomas use oxygen (O2) to convert ammonia (NH3) into nitrite, nitrite (NO2-) is already a less toxic substance for fish, however could still pose a serious problem.  Therefore in your aquarium the ammonia and nitrite concentration must remain as close to 0 parts per million as possible.

After the ammonia has been turned into nitrite, a different group of bacteria called Nitrobacter convert the nitrite into nitrate (NO3-) through a reaction with oxygen. Nitrate, unless present in extreme quantities poses no threat to your aquarium. 

Nitrate in a healthy tank does not have the tendency to accumulate to these extremes as they are processed further by plants, substrate bacteria or water changes. However when you do not do proper maintenance the nitrate concentration can climb to unhealthy concentrations. When this happens you might risk having Old Tank Syndrome. I wrote an article about that, but in short: do your water changes even if you have a lot of plants.

Where do these beneficial bacteria come from?

Both groups of bacteria needed for the nitrogen cycle occur naturally in nearly all soils and all bodies of water, including tap water. Larger amounts of these bacteria are present in filter media, the bodies of fish and in your aquarium substrate. However they are not there from the get go, the colony needs to strengthen over time.

This process, where you aquarium is essentially building its defenses against toxic ammonia, is called cycling your aquarium. It is important to cycle your tank whenever you start a new aquarium.

Cycling your aquarium

When starting a new tank, it is crucial to cultivate the proper amount of beneficial bacteria to stimulate to process ammonia into nitrate. The process of preparing your water for the arrival of your first fish is called cycling (after the nitrogen cycle) of your aquarium. Cultivating these bacteria might seem difficult but in reality takes little more than some patience. The following steps will help you prepare your aquarium for the arrival of your fish.

  1. Prepare your substrate: Bacteria love to multiply in substrate, adding substrate also makes sure that you keep a healthy dose of bacteria after changing water, as the bacteria will reside in the substrate.
  2. Add plants: Most plants will do fine in a slightly ammonia rich environment, the plant will also produce traces of waste for the bacteria to process which will stimulate their reproduction. There are many easy live plants for you to choose from, I made a list which you find here.
  3. Add an item from an earlier aquarium: Bacteria are incredibly resilient and will most likely still be present on branches, rocks, stones or plants that have been kept in an aquarium previously, by adding colonies from earlier aquariums, you can effectively speed up the process of cultivation.
  4. Turn on your filters and aeration: Bacteria cultivate more rapidly in oxygen-rich water, by creating surface movement, you maximize the multiplication of your bacteria colony.
  5. Turn on your heaters: Nitrifying bacteria thrive at temperatures between 24-30 degrees Celsius, by heating the water you exponentially increase the rate at which your bacteria can multiply. 
  6. Add an ammonia source: As nitrifying bacteria effectively use ammonia as a food source, adding a source of ammonia will increase the amount of beneficial bacteria in your water. This source can either be a product bought at aquarium stores or a small fish such as a molly or a guppy, be aware however that since the beneficial bacteria are important for the well-being of the fish, the fish might be struggling the first couple of weeks. This struggle will however ensure that all other fish will thrive in your prepared water. There is a chance your fish dies during the cycling period as the aquarium can not handle the produced ammonia yet. Therefore, I would recommend a fish-less cycle and add some store bought ammonia or some fish food.
  7. Wait, wait, wait: It is important to give your colony time to grow and start your nitrogen cycle, a period of six weeks before adding any fish is ideal.
  8. Measure and monitor the cycle: If you want to know exactly how far along your aquarium is in the cycle, it is important to measure the water parameters to see if the bacteria are converting ammonia into nitrite and finally into nitrate. This can also tell you whether your aquarium is completely cycled and ready for fish.

When is your aquarium completely cycled?

Before adding fish to your aquarium, it is important to know if your aquarium is completely cycled. After all you do not want to add beautiful fish to an aquarium which can not handle their waste yet. They will die. The most efficient way to be certain your aquarium is cycled is to test your water.

Testing your water can be done by using test kits that can be bought inexpensively at many places. While there are many test kits on the market, the best test kit that I recommend is called the API Master Kit. It is available on Amazon, check out the current price here. These DIY water test kits will help you measure ammonia, nitrite and nitrate which will tell you if your nitrogen cycle is up and running. 

How to test your water? Roughly speaking there are two varieties of test, a test using paper test-strips and a water droplet test. The paper test is the easiest of the two to perform, however, it is way less accurate and therefore can only be used as a rough indication. To measure using a test strip, simply take a glass of water from your aquarium and dip the strip in the water. Remove the strip from the water and compare the color with the colors shown in the product usage guide.

The water droplet test on the other hand requires you to measure a certain amount of aquarium water in a glass, add drops of chemicals to the water and then compare the color of the water to the colors shown in the product usage guide. There are different tests in the kit for different substances, and you can read the values a lot more accurately.

Desired parameters when tested

  • 0 ppm (parts per million) ammonia
  • 0 ppm nitrite
  • nitrate should build up over time, meaning that ammonia is immediately broken down into nitrate and finally into nitrate

Is your nitrogen cycle up and running? Congratulations, you are now ready to add your new aquatic pets to your aquarium!

Tip: Do not add a lot of fish at once. When your aquarium can only handle minor amounts of ammonia at a time, adding a lot of fish will cause too much ammonia and will raise the concentration. Instead, add just a couple of fish at a time.

New tank syndrome

Many people starting a new aquarium, experience something called new tank syndrome. 

New Tank Syndrome occurs when your aquarium is not sufficiently cycled to handle to produced waste by your fish. It’s a common misconception that a filter is all that’s needed to reduce the amount of waste in an aquarium. Although a filter is very good at accumulating particles that would make your water seem dirty, it is not sufficient to get rid of potentially dangerous amounts of chemical particles that might harm your fish. 

New tank syndrome occurs when the ammonia levels rise too high, killing or severely harming fish. The treatment of new tank syndrome is a tedious task that requires time. New tank syndrome is better prevented than treated. Although new tank syndrome can be lethal to your pets, there are some things that can be done if diagnosed on time:

  • Water changes: replace 15 to 20% of your water daily for a period of two weeks. although the build up of ammonia happens incredibly quickly, prolonged exposure to these high levels is what is dangerous to your fish.
  • Use some of the tips mentioned above to kickstart your nitrogen cycle: the problem you are facing is caused by a lack of beneficial bacteria, it is crucial to acquire those bacteria as soon as possible. It is unwise to add an ammonia source or increase the water temperature at this point, however adding aeration or perhaps adding bacteria from another aquarium will help you tremendously.
  • Dechlorinate your tap water: depending on where you live, your local tap water supplier might add chlorine to your water to eliminate disease causing bacteria from your tap water. This chlorine, however, is very capable of also eradicating the beneficial bacteria in your aquarium. Tap water can be dechlorinated using a chemical product readily available. Read more about this in this article I wrote.
  • Don’t panic: New Tank Syndrome will happen in some form or another to any aquarium keeper, from beginners to professionals. It is important to deal with this problem in the most efficient way as possible, so it is important not to hesitate and to act quickly.

In this guide to the nitrogen cycle I explained what the nitrogen cycle is, what the role of beneficial bacteria is for a healthy aquarium and how to cultivate them to get your aquarium up and running. I also explained what New Tank Syndrome is, how to avoid it and how to best treat it should it happen to you. For other topics relating to aquarium keeping, fish husbandry and other aquarium related topics, I encourage you to visit other pages on this website. Aquariumgenius.com is dedicated to regular updates with all the info you need to best care for your aquatic pets.

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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