The Planted Aquarium Nitrogen Cycle

by Apr 25, 202011 comments

So you have decided already where to place your aquarium at home, you already determined the ideal size of your tank, and what is the aquascaping design that will unleash your creativity. Should we now hunt at our local LFS (Local Fish Store) or online for the needed tank, materials, plants, fish, equipment, etc. right? Well, you can certainly do that, but before you set up your tank, let’s discuss the most important natural cycle that occurs in our aquariums: The Planted Aquarium Nitrogen Cycle.

Table of Contents

Why Discuss This Too Early?
But How Can We Establish Our Tank First?
So How Does Cycling a Tank Relates to the Nitrogen Cycle?
Do We Really Need to go Through the Science of it?
What is the Nitrogen Cycle in Nature?
The Nitrogen Cycle in our Aquariums
Aerate Your Water Always!
Wait! You said that the Nitrogen Cycle Starts With a Gas and Ends With a Gas, Where is the Nitrogen Gas at the Start and End?
Closing Remarks
Pearl Gourami

The Planted Aquarium Nitrogen Cycle (You Are Here)

It starts with a gas and ends with a gas. Basically, the Nitrogen Cycle is processes that convert the atmospheric Nitrogen gas (inorganic) into other forms of organic Nitrogen and then back to gas again. Those processes are carried out naturally by microbes for energy-harvesting or food.

The Fastest Method

The Fastest Method of Cycling our Planted Aquariums involves using your old substrate, gravel, hardscape, filter, filter media, part of the old water from your old aquarium to our new planted aquarium.

But this needs careful planning and execution for this to be successful. In this article, we will tackle step by step how to carry out this method.

My 3rd Re-scape Lemuel Sacop Philippines

Betta Fish

Traditional and Modified Traditional Method

The Traditional Method of Tank Cycling is the oldest method used by our grandparents when technology was not as advanced as we do now and involves cycling our planted tank with fish in it to jumpstart the Nitrogen Cycle.

Many consider this method as inhumane, sacrificing our fish. Still, nowadays, there are live-nitrifying bacteria products that can help speed up this process and make this method safe for our fish.

Fishless Method

For those willing to wait and love to watch their plants grow and become lush before adding the fish, this method is for you.

It is called the Fishless Method of Tank Cycling, which is self-explanatory. We will cycle our planted aquariums with no fish.

Fissidens Moss Grown Emersed Fishless Aquascaped by Charles Edward David

Why Discuss This Too Early?

Because it is easy for a beginner to get too excited to set up their first planted tank, set up the filter and lighting, begin aquascaping, planting, filling it with water, putting the fish in, etc., then meet the consequences.

New Tank Syndrome – this usually happens when you put fish/fishes, snails, shrimps in almost immediately after setting up your tank, harming the fish/es, snails, or shrimps and can even result in their untimely demise.

Pearl Gourami

This is due to toxic substances’ (such as ammonia and nitrite) rising levels because your filter, filter media, and all the hard surfaces in your tank haven’t developed the beneficial bacteria yet to deal with these toxic substances.

So to avoid New Tank Syndrome, we recommend establishing your tank first before adding the faunas.

But How Can We Establish Our Tank First?

Establishing our tank or “Tank Cycling” means we have to establish these beneficial bacteria to colonize on our filter media within our filter.

The different types of filtration and filter media that we can use for our planted aquariums are discussed in this article; go here.

These beneficial bacterias can also live on every hard surface inside your aquarium, including the soil/aquasoil, hardscapes like rocks and driftwood, your submersible pumps, and your filter’s intake outtake tubes (the part that is submerged in water), even on the inside glass wall. You might be surprised by this, even on the plants themselves and some free-floating in water. Basically, everything submerged in your tank can be home for your good bacteria. Everything act as a filter, specifically, biological filtration media.

Nature Style Aquascaped by San Mig Chad Philippines

Nature Style Aquascaped by San Mig Chad Philippines

However, we have to wait for the Tank Cycling to finish before putting in the faunas (fish, snails, shrimps). This may take a few weeks to months. What??? Well, at least you still have your plants, and you got to see them grow and lush before adding the fish. What do you call an aquarium with just water on it?

Fortunately, there are ways to induce it and speed up the process, and we will discuss them thoroughly in the next article.

So How Does Cycling a Tank Relates to the Nitrogen Cycle?

Because these toxic substances (ammonia and nitrite) I mentioned earlier are all organic forms of Nitrogen, it is essential to know where they come from and how they are converted to a less harmful substance in our aquariums. This is for the well-being of our fish and plants.

Hardscape Diorama Aquascaped by Rennier Katigbak Philippines
Hardscape Diorama from Setup to Finish Aquascaped by Rennier Katigbak Philippines
Hardscape Diorama - Aquascaped by Rennier Katigbak Philippines

Hardscape Diorama Styles Aquascaped by Rennier Katigbak Philippines

Do We Really Need to go Through the Science of it?

I honestly admit, when I started my first fish-only tank more than 3 years ago, I didn’t perform any tank cycling, nor did I researched the Nitrogen cycle. Maybe I was just fortunate that no fish died (I chose the hardiest fishes anyway), or it might be attributed to our “magic deep-well” (I will describe this magic deep-well of ours and why I think it helped my fish survived the no Tank Cycling)! I didn’t know better back then, so I am seriously not advocating no tank-cycling and risking your faunas. It worked for me, but it may not work for you.

Cichlids Variety

And even when I started my first planted tank, I still didn’t perform any tank cycling, despite researching it and even after some experienced hobbyists told me to do so. Why?

Because I used my old ceramic decorations, gravel, some shells, and the filter media that I used from my old 15 gallons fish only tank to my new 35 gallons planted tank. I used the same water source (deep-well), and I just transferred the fishes after filling it up with water. No casualties.

Using your (or from a friend) old filter media, gravel, aquasoil, hardscapes, and even parts of the old water is the fastest way to cycle a new tank because they already have the beneficial bacteria that we need. Just don’t allow them to dry out as it will kill your good bacteria. Use your old tank water for that.

And no, we don’t need to get through the science of it. All the complex scientific terminologies, chemical symbols, nor balancing chemical equations, etc. Really?

So please don’t worry, just relax, sit tight, and just read further down below for a merry-go-round ride that is the Nitrogen Cycle in our aquariums.

My First Beginner Planted Aquarium Using the same Gravel, Shells, Filter, Filter Medias, Decorations, etc.

My First Beginner Planted Aquarium Using the same Gravel, Shells, Filter, Filter Medias, Decorations, etc.

What is the Nitrogen Cycle in Nature?

It starts with a gas and ends with a gas. Basically, the Nitrogen Cycle is processes that convert the atmospheric Nitrogen gas (inorganic) into other forms of organic Nitrogen and then back to gas again. Those processes are carried out naturally by microbes for energy-harvesting or food.

Yes, I said microbes. Those micro-organisms/bacteria that we often disregard (because we cannot see them in our naked eye?) have a big impact on the Earth’s ecosystems and the Nitrogen Cycle itself. Our aquariums are an enclosed ecosystem, and those bacteria help to establish our tanks.

This is the closest you can get with Mother Nature, not your Nature aquascape or your Walstad tank. One of the most important cycles in Nature is happening in your aquarium, and it is carried out by micro-organisms that you cannot even see. We often neglect how important they are.

The Nitrogen Cycle in our Aquariums

This can be visualized and explained by the diagram below. This diagram represents a fish only tank.

The Nitrogen Cycle in Our Aquariums Without Plants

To simplify this Diagram for you:

1. Our aquarium is very much like a septic tank for our faunas (fish/es, snails, and shrimps). Whenever they excrete, or you are overfeeding and start to decay, Ammonia is produced. When faunas die and start to decay, they will also produce Ammonia, lots of it actually until they are removed.

2. Ammonia is deadly to our faunas. Once detected, beneficial Nitrosomonas Bacteria will start to colonize in our aquarium and filter media and will breakdown Ammonia into Nitrites.

3. Nitrites are still deadly to our faunas. Once detected, beneficial Nitrobacter Bacteria will start to colonize in our aquarium hardscapes and filter media and will breakdown Nitrites into Nitrates. Both beneficial bacteria need an aerobic environment to breakdown these toxic substances. Aerobic means an environment with lots of oxygen, just like you need oxygen when you are doing your aerobic exercises.

4. Nitrates are less harmful to your faunas at low levels.

5. Your faunas will continue to eat and produce more waste; thus, more Ammonia then is converted to Nitrites and to less harmful Nitrates. Your Nitrate levels begin to go up. In freshwater planted aquariums, we should keep the Nitrate level safely from 0 to 40 ppm (parts per million).

6. Anything above 80 ppm Nitrate levels, depending on your fish species, Nitrates will begin to affect your faunas or can become lethal. Excess Nitrates can be removed by regular water change or by using live plants.

Aerate Your Water Always!

So always provide lots of surface water agitation in your aquarium, not just during tank cycling, but every time, and even when injecting CO2 (balancing your CO2 injection and providing water surface agitation is discussed here). This can be achieved by the out-take tube of your filter or using wave-makers or using aquarium/computer fans directed towards your water surface.

Your beneficial bacteria always need oxygen to break down the toxins in our aquariums. Your faunas need oxygen, and your plants can give off oxygen when they respire during lights on, but our plants need oxygen during lights off too. And because your water temp is cooler by blowing air into your water surface (evaporative cooling), the capacity of your water to hold dissolved oxygen increases.

Aerating your water via aquarium fans will cool your water temperature and improves the nutrient and CO2 intake of your plants plus mosquitoes hate laying their eggs in moving water. And even if they manage to do that, your faunas can take care of the larvae. Some if not most algae hate cool waters and moving water looks more natural than stagnant.

Benefits of Aerating Your Water Using Fans. Please also like and subscribe.


The bacteria that convert Ammonia into Nitrites (Nitrosomonas) populate/reproduce much faster than the bacteria that convert Nitrites into Nitrates (Nitrobacter). Keep this in mind when you are cycling your planted aquarium. Depending on the method of tank cycling you are planning to undertake (which we will discuss in-depth in the succeeding articles), you may experience rising and lowering Ammonia levels. At the same time, the Nitrites keeps on accumulating for a week or two.

This also explains the bacterial bloom (cloudy effect) that happens when you have Ammonia Spikes (dead faunas, or neglected maintenance, or you use chlorinated water into an established tank-killing off your good bacteria), the Nitrosomonas bacteria can overproduce. Once the Ammonia spike is taken care of by the correct population of bacteria, the excess bacteria die, and that is when the cloudy water starts to clear.

Please remember that you don’t have to memorize the beneficial bacteria names that will break down Ammonia into Nitrite and then into less harmful Nitrates and the scientific terminologies. The most important thing, for now, is you know the part of the Nitrogen Cycle in your aquarium that will ultimately – can benefit your faunas and plants.

The Planted Aquarium Nitrogen Cycle

This is the Diagram when you have a Planted Tank. It is basically the same as the 6 steps above, but the plants will help to reduce your nitrates too, to some extent. The plants can also contribute to the Ammonia when they shed leaves or if they are unhealthy and dying, and those start to decay.

Cycling your aquarium refers to the process of making sure that you have enough beneficial bacteria to breakdown the most harmful (Ammonia and Nitrite) substances faster than they can be produced.

Also, the rate at which plants consume your excess Nitrates depends on how heavily your tank is planted. Also, did you know that plants can consume Ammonium directly? There are experimental studies that most aquatic plants tend to prefer Ammonium because they can use it immediately to make their own food. As oppose to consuming Nitrates, plants still need to convert it back to Nitrites and then convert it back to Ammonium within their cells. This requires more energy for the plants to make the nitrate useful for them.

My Heavily Planted 35 Gallons Tank

My Heavily Planted 35 Gallons Tank

Plants can still use nitrates, albeit, slow due to the energy required to convert it back to ammonium. That is why I said above that plants can reduce your excess nitrates, just to some extent only.

But what is Ammonium, since I already mentioned it. The term Ammonia actually refers to two compounds held in equilibrium with each other in our aquarium water: Ammonia un-ionized (NH3) and ionized Ammonium (NH4+). The toxicity to Ammonia for our faunas is primarily attributed to the NH3 part. When you measure Ammonia with a test kit like the API Test Kit, you measure the total of both.

Their equilibrium ratio depends on the pH and temperature of your water. The higher your water pH than 7 (neutral) and temperature, the more NH3 and vice versa. This means that in high pH than 7 (alkaline) and elevated temperatures, NH3 (Ammonia un-ionized) is greater in numbers than NH4+ Ammonium (ionized), which is very lethal to your faunas.

As an example, when your fish gets shipped cross-state or cross-countries, they are packed in a plastic bag with no filtration obviously, no gas exchanges in the water with air, etc. When they poop, it will start to decay quickly due to the elevated temperatures and will turn into Ammonia.

Ammonia is an acid and that will drop the pH of the water down. When the pH of the water drops, Ammonium is more prevalent in the confined water, which is less lethal than un-ionized Ammonia. The nutrients water parameter of our planted aquarium is discussed in-depth in this article, go here.

Amazon Frogbit

I’m sorry, I couldn’t help it. Don’t worry about these chemical symbols and scientific terms. The important bits are:

  • Both Ammonia and Ammonium are always present in our aquariums. If something organic is decaying, they are always there. Ammonia is the toxic one, while Ammonium is less toxic.
  • Ammonia will be breakdown by beneficial bacteria into Nitrites and then Nitrates, while Ammonium will be consumed by your plants directly with no byproducts as long as they are healthy.
  • This is why Tank Cycling is faster if you have plants.

Did you know that the good bacteria can also thrive in your plants as well? They actually can colonize your plants’ roots.

Also, organics (such as dead plant matter, fish excrements, dead faunas) and uneaten fish food in your tank don’t just magically turn into Ammonia/Ammonium. They have to decay first. But before decaying, it releases proteins, enzymes in the water.

You might be wondering about the oil films at the surface of your water? Those are proteins released by organics in your tank.

Iwagumi Style Aquascaped by Michael Yap Philippines

Iwagumi Style Aquascaped by Michael Yap Philippines

Wait! You said that the Nitrogen Cycle Start With a Gas and Ends With a Gas. Where is the Nitrogen Gas at the Start and End?

The Nitrogen Cycle in our Aquariums refers to only parts of the Nitrogen Cycle because it is missing some processes. However, other missing beneficial bacteria will break down Nitrates into Nitrogen Gas and back into the atmosphere, completing the cycle and starting it again. And this good bacteria is not often mentioned in publications and other sites.

These bacteria’s metabolism is anaerobic, which means they can only survive in an environment void of oxygen or very little oxygen. This bacteria is not always present in every single aquarium. Is there a place in our aquarium where oxygen does not exist?


    They can only survive down below in the deepest of substrates. There must be a very slow exchange of water through the substrate. Most experienced Marine aquarium keepers already know about this as it is easier to employ this with a deep layer of sand. They can also colonize in the very insides of porous biological filtration media and hardscape such as lava and pumice rocks where there are little to no water flow and very little oxygen.

    Have you ever wondered what are those rare big bubbles rising quickly into the water surface from your substrate? Yes, those are N2 Nitrogen gas, which is inert and will not affect your fish and water parameters. The process of breaking down Nitrates into Nitrogen gas is called Denitrification.

    Shrimp Substrate
    Nature Style Deep Substrate Aquascaped by Armel Adman David Philippines

    Nature Style Deep Substrate Aquascaped by Armel Adman David Philippines


    Understanding the Nitrogen Cycle in our aquariums is very important for the well-being of your faunas and floras. It is a natural cycle that converts Nitrogen’s different forms/compounds into less harmful forms in our aquariums.

    The basic points are that toxic Ammonia from our faunas’ waste is converted to Nitrite, which is also toxic, and then converted to less harmful Nitrates, which can be removed by plants and regular/weekly water change.

    Understanding the Nitrogen Cycle also forms our understanding of the importance of Tank Cycling for newly setup planted aquariums.

    Want to Explore More?

    Osmosis in Planted Aquariums

    Osmosis is the process in which any solvent moves through a membrane in a direction from lower concentration to higher concentration that tends to equalize the solutes’ concentration on both sides. The membrane should be semi-permeable and good examples are the cells of the aquatic faunas and plants.

    Paludarium Ideas

    A Paludarium is a type of vivarium that contains water and land in the same environment or encasement. The design can simulate natural habitats such as rainforests, jungles, streams, riverbanks, and bogs. In a Paludarium, part of the aquarium is underwater, and part is above water.

    Rimless or Braced Tanks

    Have you heard of Rimless or Braced tanks before? This article will help you with your decision if you want a Rimless Tank or a Braced Tank for your planted aquarium.

    What to Look for in a Planted Aquarium Filter

    Having plants in an aquarium is not a justification for having no filtration. The plants cannot do it alone, even in the most natural of systems.

    Less water volume means the water gets polluted faster, and your water parameters can go out of whack in an instant, most especially if your planted aquarium is not cycled yet. And this is augmented if you have a smaller tank (nano tanks). So choosing your filter is very critical.

    Water Parameters

    Nutrients – Planted Aquarium Water Parameters

    Our aquarium is very much like a septic tank for our faunas (fish/es, snails, and shrimps). Whenever they excrete, or you are overfeeding, and those organics started to decay, or when dead plant matter decays, Ammonia is produced. When faunas die and decay, they will also produce Ammonia, lots of it actually, until they are removed. This causes ammonia levels in our tank to spike.

    Taiwanese Style with Lego Crab Aquascaped by Ian Garrido Philippines

    Taiwanese Aquascaping Style

    The Taiwanese Style of Aquascaping combines the elements of Nature, Iwagumi, or Dutch styles, but the most bizarre feature is using figurines, toys, etc. in the tank to create a sense of life. Just make sure that the ‘object’ you will use will not leak any harmful substances in the water column outright and as time goes by.

    Closing Remarks

    I hope you enjoyed this article. If you have additional questions or want to share your experiences with the Nitrogen Cycle in our Planted Aquariums, please leave a comment below.

    Next, we will be discussing the fastest method of cycling our planted aquarium.


    1. Dave

      Hallo there Lemuel, 

      Thanks a lot for this post. It came just when I needed it.

      I am just setting an aquarium and I am in my initial stages. I have been researching a lot on this as I want it to be perfect. The nitrogen cycle was mentioned to me in a few previous research posts I was reading. I saw how the knowledge of it was stressed a lot and I thought I should look at it closer. And that is how I landed here. Thanks a lot for the detailed info here. I have even bookmarked your website to be getting more tips and advice on my project. I really appreciate the value of help you have offered here. Good day!

      • Lemuel Sacop

        Thank you Dave for the appreciation of my article. Please watch out for more articles coming soon.

    2. Antonio


      Thank you for clearly explaining  the nitrogen cycle and its relevancy  to fish tanks. It is important to know how ammonia generated by the  excrement, fish food and other organic matter is converted to nitrites and then nitrates via the action of bacteria. It is right to get your aquarium in balance, so that  the fish are unharmed from too potential toxins. I can imagine you have to be aware at what conditions  the ammonia is generated and how to minimise the bacteria inside the tank to stop nitrites and nitrates are produced. It is tricky to get the pH, ammonia , nitrites and nitrates right as this is so dependent  on some many variables, some can be controlled  by you and others you cannot control. I have been taught not to rush in buying my tank and all the accessories. You mentioned some fish are more tolerant of high  ammonia and nitrites, can you tell me what kind?



      • Lemuel Sacop

        Hi Antonio,

        Thank you for appreciating my article. Yes, there are a lot of variables and science in our aquariums but I don’t want to bombard our readers with a lot scientific terminologies yet, as they might get bored quickly. Ammonia is inevitable, it will be created in our aquariums whether we like it or not and it will start the Nitrogen Cycle in our little ecosystem. So it is really important to know where it comes from and how it is converted into less harmful form. As for your question, they are just a couple of mollies and non-fancy goldfishes, and some White Skirt Tetras but it might just be attributed to our magic deep well.

        I will describe that magic deep-well in a future article and why I thought it helped a lot with my fishes even without tank cycling.

    3. Anthony Hu

      Thank you for your post. It is informational and educational. My son loves fishes and want to have fish tank. I promise to buy fishes and fish tank for him. I thought it is just that simple. After reading your article, I realize that there are so many science behind the fish tank.

      I particularly like your description on Why Discuss This Too Early, which provide foundation for the management of fish tank for the future.

      Your article prevents me from the New Tank Syndrome. I bookmarked your webpage and follow your instruction to establish the tank and then add the fishes.

      • Lemuel Sacop

        Hi Anthony,

        Thank you for the appreciation of this article and providing your experience. I am glad you are starting your son on the responsibilities of keeping an aquarium at home. If you have more questions please don’t hesitate to ask.

    4. Russ

      I really enjoyed your article. I didn’t know there was so much to think about when it came to prepping a tank. I really want one in the walk but I’d imagine cleaning it is a nightmare.

      • Lemuel Sacop

        Thank you Russ for the appreciation about my article. Actually, cleaning and maintaining these planted tanks are actually easy. Once a week 25 % water change and some occasional trimming of your plants are all that it takes.

        Remember, your plants can use the fish wastes as their own fertilizer so you don’t even have to vacuum your substrate often.

    5. Walter Zessin

      This post is very informative and thought-out. I have never had nor probably will ever have a fish tank or fish. But to anyone that is wanting to or that does. They need to read this if there not sure about something. Five stars man keep it up!

      • Lemuel Sacop

        Hi Walter,

        Thanks for the appreciation about my article. I hope in someways, I was able to help you in your decision to start your very own planted aquarium at home. Please watch out for more articles coming soon.

    6. Cordelia

      This is such a great resource for newbies like me! I have been looking into getting an aquarium and there is just so much confusing information snippets out there, and my head started spinning from all the different pieces of advice. Having a solid understanding of the Nitrogen cycle just helped me clear my head so much! I am so happy right now


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