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The Science Behind Nitrites & Nitrates Dynamics: Clear Water & Healthy Fish

Unveil the secrets behind nitrites and nitrates dynamics, and learn how to maintain crystal-clear water and healthy fish in your aquarium.

DEEP DIVE GUIDE - Discover the Science of Aquarium Filtration

Maintaining water quality is crucial for a thriving aquatic ecosystem, and understanding the science behind aquarium filtration is essential for achieving clear water and healthy fish. At the heart of this process is the nitrogen cycle, a series of chemical reactions that convert harmful waste products into less harmful substances. In this article, we will explore the different types of filtration—mechanical, chemical, and biological—and discuss the importance of understanding nitrites and nitrates dynamics for maintaining a well-balanced aquarium.

The Nitrogen Cycle

It’s invisible to the naked eye…

Yet, within your aquarium, a vital cycle is taking place. We’re talking about the nitrogen cycle. For a beginner, the nitrogen cycle might seem like a complex idea to grasp. But fear not, today, we’ll simplify the entire cycle into manageable pieces.

By the end of this deep dive guide, you’ll have a thorough understanding of the nitrogen cycle – even if you’ve never owned an aquarium before!

So, without further ado, let’s dive right in! Don’t worry, some of this stuff may sound complicated, but as you read further, you will see me break it all down for you with easy to look at diagrams.

Definition & Importance in Aquariums

The nitrogen cycle is a series of biological processes that convert toxic ammonia, produced by fish waste and decaying organic matter, into less harmful substances like nitrites and nitrates. A well-established nitrogen cycle is essential for maintaining water quality and supporting healthy fish.

Stages of the Nitrogen Cycle

The nitrogen cycle consists of three main stages:

  • a. Ammonia production: Fish excrete ammonia as a waste product, and decomposing organic matter also releases ammonia into the water.
  • b. Nitrite production: Beneficial bacteria called Nitrosomonas convert ammonia into nitrites, which are also toxic to fish.
  • c. Nitrate production: Another type of bacteria, Nitrobacter, converts nitrites into nitrates, which are less toxic and can be absorbed by plants or removed through water changes.

Factors Affecting the Nitrogen Cycle in Aquariums

Various factors can influence the nitrogen cycle, including water temperature, pH, oxygen levels, and the amount of waste produced by fish and other organisms.

Nitrogen Cycle (Information Table)

StageProcessChemical ConversionBacteria InvolvedEffects on Aquatic Life
Ammonia ProductionFish waste, uneaten food, plant debris decompositionOrganic matter → Ammonia (NH3)N/AHighly toxic
Nitrite ProductionOxidation of ammoniaAmmonia (NH3) → Nitrite (NO2-)NitrosomonasModerately toxic
Nitrate ProductionOxidation of nitriteNitrite (NO2-) → Nitrate (NO3-)NitrobacterLess toxic, plant nutrient

The Nitrogen Cycle (that you can see)

Recall when I mentioned that the nitrogen cycle was unseen Well, that’s not entirely accurate – some aspects of it are indeed visible. In reality, you’re actively involved in the nitrogen cycle without even knowing it! Let’s explore the components of this cycle that are visible to us…

  1. You provide food to your fish, and any leftover food turns into waste.
  2. Your fish eats the food and poops – more waste.
  3. Plants in your aquarium shed dead leaves – more waste.
  4. This waste begins to build-up.
  5. Then you perform a water change to clean it.

Simple right?

The full nitrogen cycle is only a little more complicated than this. Let’s put the missing pieces of the puzzle together – the parts of the nitrogen cycle that you can’t see.

aquarium filtration
aquarium filtration

The Complete Nitrogen Cycle

  1.  You provide food to your fish, and any leftover food turns into waste.
  2.  Your fish eats the food and poops – more waste.
  3.  The waste in your tank builds up.
  4.  As the waste starts to break down and decay, it releases ammonia.
  5.  Bacteria then converts the ammonia to nitrite.
  6.  A different type of bacteria then converts the nitrite to nitrate.
  7.  Plants utilize nitrates for growth, reducing a minor portion in the water. Dead leaves from the plants also contribute to waste.
  8.  A large amount of nitrates are removed with your water change.



This is the full nitrogen cycle. You see? I told you it wasn’t that difficult to understand! Even though it’s not visible, this entire process is continually happening in your aquarium.

When someone mentions cycling your fish tank, they’re referring to the process that occurs in steps 4, 5, and 6 – ammonia, nitrite, and nitrate – as illustrated in the diagram above. These three steps form the core fundamentals of fishkeeping.

Honestly, it’s amazing how many problems can be linked to ammonia, nitrite, and nitrate – these invisible chemicals are true troublemakers. Unless you intend to become a fish serial killer, it’s crucial to thoroughly understand the nitrogen cycle. Now that you’ve grasped the basics, let’s expand upon this knowledge. Don’t worry, we’re almost there!

Just a little further, and you’ll know everything about the nitrogen cycle. It’ll be worth it when you use this knowledge to raise happy and healthy fish! So, let’s examine the unseen aspects of the nitrogen cycle more closely.

Amonia (Harmful)

Let’s break this down a little for you now. 

Although it might not be the initial step, ammonia is often regarded as the starting point of the nitrogen cycle. Ammonia enters your aquarium as waste breaks down.

Waste consists of:

  • Fish poop
  • Unconsumed fish food
  • Dead & decaying plant pieces
  • Decaying algae
  • Unclean filters (learn more about choosing the right filter system for you here)
  • Fish respiration

Essentially, if it’s organic and starts to decay, it has the potential to release ammonia into your aquarium. Ammonia is then transformed into NITRITES.

Nitrites (Harmful)

The conversion from ammonia to nitrite doesn’t occur by itself. It gets assistance from bacteria called nitrosomonas. Don’t stress about memorizing that name, all you need to know is that this specific type of bacteria consumes ammonia. When it does, it generates nitrites.

Once a colony of this bacteria is established, it can consume ammonia as quickly as it’s produced from decaying waste. The issue is that nitrites are highly toxic to fish. Thankfully, another kind of bacteria then transforms the nitrites into something much less harmful – NITRATES.

nitrite to nitrate

Nitrates (Harmless)

Be cautious not to mix them up— the names are strikingly similar, with just one letter distinguishing the two. Nitrates are formed when a second type of bacteria – called nitrobacteria – consumes the nitrites. Again, once a colony of this bacteria is established, it can consume nitrites as quickly as they’re produced. Nitrates are much less harmful to your fish, as long as the levels don’t get out of hand.

While plants and some bacteria help remove nitrates from the water, in most aquariums, it won’t be enough to prevent nitrates from reaching dangerous levels. Nitrates are considered the endpoint of the nitrogen cycle since they continue to build up until you intervene and perform a water change. This is one reason why you need to carry out regular water changes – to keep nitrate levels in check.

Congratulations, you’ve successfully learned all you need to know about the nitrogen cycle!

nitrite to nitrate

The Delicate Balance of the Nitrogen Cycle

It’s essential to understand that the nitrogen cycle is actually a fragile equilibrium. A significant aspect of fishkeeping involves maintaining a healthy nitrogen cycle. When this balance is disrupted, major problems can arise quickly. A spike in ammonia, nitrite, or nitrate can throw your aquarium into turmoil.

For example, if you clean your filter and accidentally kill all the bacteria inside, ammonia and nitrite levels in your tank will spike without the bacteria to break them down, possibly harming your fish. Similarly, a fish tank with an excessively high bioload might generate ammonia and nitrites faster than the bacteria can process them. 

As you can see, an unbalanced nitrogen cycle indicates that something else is amiss in your tank. 

AquaManLife Fact: Promoting the growth of this bacteria in your filter, so it removes ammonia and nitrites from your aquarium, is called biological filtration.

Monitor the nitrogen cycle in your tank by regularly testing your ammonia, nitrite, and nitrate levels – using an aquarium test kit. If you can achieve a harmonious balance with the nitrogen cycle (which we know you can!), you’ll be rewarded with happy and healthy fish. 

Nitrogen Cycle in a New Tank

Recall that I mentioned there are two types of bacteria involved in the nitrogen cycle? One transforms ammonia into nitrites, and another changes nitrites into nitrates. 

AquaManLife Fact: The bacteria that convert ammonia to nitrites and nitrites to nitrates are known as nitrifying bacteria.

A new aquarium doesn’t have enough of these bacteria to break down ammonia and nitrites in your tank. The result is water that can make your fish unwell or, even worse, kill them outright. That’s where tank cycling comes into play.

When you cycle your aquarium, you’re essentially waiting for these two bacteria to multiply until they can consume ammonia and nitrites as fast as they’re produced – keeping their respective levels at zero. So now that you’re familiar with the nitrogen cycle and its significance in a healthy aquarium, it’s time to dive in and experience it firsthand by cycling your aquarium! You can read more about cycling your fish tank in this article “The Magic of Cycling Your Fish Tank“.


Maintaining Clear Water & Healthy Fish

Importance of Water Clarity for Fish Health

Clear water is not only visually appealing but also crucial for fish health. It allows light to penetrate the water, which is necessary for plant growth and photosynthesis, and helps maintain stable water temperatures.

Factors Affecting Water Clarity

Various factors can affect water clarity, including suspended particles, dissolved organic matter, and algae growth.

Strategies for Maintaining Clear Water

Effective mechanical filtration, regular water changes, and controlling nutrient levels can help maintain clear water in an aquarium.

Monitoring & Maintaining Water Quality for Fish Health

Regular testing of water parameters, including ammonia, nitrite, nitrate, pH, and temperature, is essential for maintaining a healthy aquatic environment. Adjusting filtration, water changes, and other aquarium management practices can help maintain optimal water quality.

Final Thoughts

Understanding the nitrogen cycle and the roles of nitrites, nitrates, and ammonia is essential for maintaining a healthy and thriving aquatic environment. By closely monitoring the levels of these compounds and promoting the growth of beneficial nitrifying bacteria, you can achieve crystal clear water and ensure the well-being of your fish.

Remember that the key to success lies in maintaining the delicate balance of the nitrogen cycle. Regular testing, water changes, and properly managing the bioload in your aquarium will go a long way in keeping the water quality pristine and your fish happy and healthy.

Armed with this knowledge, you’re now better prepared to create a thriving and vibrant underwater world for your aquatic pets to enjoy. Keep learning, stay vigilant, and enjoy the rewarding journey of fishkeeping.


What is the nitrogen cycle, and why is it important for my aquarium?

The nitrogen cycle is a natural process that breaks down harmful waste products into less toxic compounds, essential for maintaining a healthy aquatic environment.

How do nitrites, nitrates, and ammonia affect my fish?

High levels of ammonia and nitrites are toxic to fish, while high nitrate levels can cause stress and health issues.

What are nitrifying bacteria, and how do they help my aquarium?

Nitrifying bacteria convert toxic ammonia to nitrites and then to less harmful nitrates, keeping your fish safe and healthy.

How can I promote the growth of beneficial bacteria in my tank?

Cycling your aquarium and using a good quality filter media and plants can encourage the growth of beneficial bacteria.

How often should I test my aquarium water for ammonia, nitrite, and nitrate levels?

You should consider testing your water regularly, especially during the initial cycling period. After that, aim to test every 2-4 weeks.

What are some signs that my nitrogen cycle is unbalanced?

Cloudy water, poor fish health, or sudden spikes in ammonia, nitrite, or nitrate levels could indicate an unbalanced nitrogen cycle.

How do water changes help maintain the nitrogen cycle?

Regular water changes help remove excess nitrates, reduce harmful substances, and maintain a stable and healthy environment.

Can plants help with the nitrogen cycle?

Yes, live plants can absorb nitrates and help maintain a balanced nitrogen cycle in your aquarium. You can read more about different plants and aquascaping, we even have an article about unconvential aquatic plants.

What is the ideal nitrate level for my aquarium?

Ideally, nitrate levels should be below 20 ppm, but the optimal level depends on the specific species of fish and plants in your tank.

How long does it take to cycle a new aquarium & can I speed up the process?

Cycling a new aquarium can take anywhere from 2 to 6 weeks, depending on various factors such as tank size, temperature, and bacteria sources. Using a bacteria starter or adding filter media from an established aquarium can help speed up the cycling process, which you can read more about this in our article called “The Magic of Cycling Your Fish Tank“.

What should I do if I notice a spike in ammonia, nitrite, or nitrate levels?

Perform an immediate water change, test your water quality, and assess the potential causes, such as overfeeding, a dead fish, or a malfunctioning filter. You can always contact us right away and we are happy to offer some advice. Or pop over to our community page where you can interact with other like minded aquarists!

Aquarium Cycling FAQ

If you have any other further questions about anything aquatic related, please do not hesitate to contact us right away! Stay tuned – we will be starting to load incredibly helpful and useful videos on the AquaManLife.com YouTube channel & Facebook, so keep a look for that coming!