The Nitrogen Cycle: Understanding Biological Filtration

September 11, 2020
September 11, 2020 Phil Overton

Understanding the importance of the nitrogen cycle is a key component to maintaining a successful aquarium, and is often confusing to people new to the hobby.  Avoiding situations that may disrupt the completion of the nitrogen cycle will go a long way in maintaining a healthy aquarium.

zebra Angelfish (Pterophyllum scalare) in a tropical aquarium

What Is the Nitrogen Cycle?

The nitrogen cycle, which occurs in both freshwater and saltwater systems, is a series of naturally occurring biological processes whereby the harmful byproducts of decaying organic matter (ammonia) are ultimately converted into less harmful species (nitrates and/or nitrogen gas.)

It starts when ammonia (NH3 or NH4) enters the fish tank (sources of ammonia are listed below).  Next, naturally occurring beneficial bacteria convert ammonia to nitrite (NO2) and then nitrite to nitrate (NO3).  In some conditions, nitrate is further converted into nitrogen gas (N2), which is then released from the tank.

Ammonia  –>  Nitrite  ®  Nitrate  ®  Nitrogen Gas


3d structure of Ammonia, also known as azane, a compound of nitrogen and hydrogen. The simplest pnictogen hydride, ammonia is a colourless gas with a characteristic pungent smell.

The nitrogen cycle begins with ammonia, which enters the aquarium as a byproduct of decaying food and plant matter. This occurs when nitrogen—an essential nutrient to life that is included in all living matter and is also a building block of proteins—breaks down, turning proteins into ammonia.

These ammonia-generating products include:

  • digestive waste products of fish
  • uneaten fish food
  • dying plants including algae
  • dead animal matter

Additionally, as a byproduct of a fish’s metabolic process, ammonia is excreted through their gills.

As the level of ammonia increases in the water, the water quickly becomes toxic to your fish. Ammonia can cause your fish to lose its appetite and become lethargic.  It will also inflame its gills, damage its eyes and ultimately cause severe-enough damage to its gills that it becomes difficult for the fish to get oxygen.


As part of the next step in the nitrogen cycle, beneficial bacteria convert the highly toxic ammonia into nitrites. Although less harmful than ammonia, nitrites are still harmful.  Nitrites will enter the fish’s blood stream and interfere with the blood’s capacity to carry oxygen, which could eventually lead to its death.


Nitrates thin line icon. Vector illustration for food packaging.

Beneficial bacteria will next convert nitrites into nitrates. Depending on the types of aquatic life in your aquarium, the acceptable nitrate levels will vary; however, almost all aquarium residents experience detrimental injuries when exposed to high nitrate levels.

High nitrate levels can cause your fish to be vulnerable to diseases and experience kidney damage, decreased fertility, poor growth, and a reduced lifespan. There are several ways to reduce the nitrate levels in your aquarium, however beneficial bacteria can also help if you create the right environment for them.  (See more on the removal of nitrates below.)

Beneficial Bacteria

Beneficial bacteria are the key component to the nitrogen cycle. They will grow naturally in your tank if the required nutrients are present (e.g. nitrogen compound, oxygen, carbon source, etc.).  These bacteria can take anywhere from one to six weeks to become fully established and convert ammonia all the way to nitrate; however, there are also options that can speed up the cycling process. One such option includes adding beneficial bacteria to your system. The most common aquarium bacteria starters come in liquid form and leads to a quick colonization of good bacteria. You can also use a piece of filter media from an established tank to seed the bacteria into the new tank.

The Role of Biofilm

Beneficial Bacteria colonies develop and live in a biofilm that grows on all available surfaces throughout the tank, and the larger the surface area available for the biofilm to inhabit, the larger the overall capacity of the system to handle ammonia will be. If the surface area is limited, the bacteria and biofilm will compete for space. This causes the biofilm to build up and, in the process, kills off the lower layers of the biofilm. It is recommended for hobbyists to supplement the limited surface area in an aquarium (i.e. rocks, gravel, decorations) by using filters and biofilter medias with vast useable surface area, which provides ample places for bacteria to grow.

Biofilm containing bacteria Klebsiella, 3D illustration. Gram-negative rod-shaped bacteria which are often nosocomial antibiotic resistant

Typically in aquarium filters, there is a section devoted to the biological filtration. The biofilter media used here often includes sponges or floss, ceramics, and even sand. When choosing a biofilter and biofilter media, it is important that enough surface area is provided for the biofilm and beneficial bacteria to grow on. Having a large surface area is essential because, first, you do not want the media to become clogged with its own biofilm, and second, you want extra capacity for biofilm growth in case there is an upset to the system, such as a decaying fish that was not removed, or even if you want to house a higher fish load in the tank.   Click here to read about common biofiltration issues.

How to Remove Nitrates in an Aquarium

The most common way to lower nitrates in your aquarium is through water changes which can be time-consuming and expensive. Another way is by adding plants or algae that use nitrates as a fertilizer. A third means utilizes beneficial anaerobic bacteria which thrive in low oxygen environments and will convert nitrate into nitrogen gas (N2). This must occur in regions with low oxygen, that is, where the oxygen has been used up from the first two cycling steps.  Biomedias with intricate pore structures have a greater chance of having low oxygen regions. When successful, nitrogen gas will form and will release from the tank.

Understanding MarinePure® Biofilter Media’s Role in the Nitrogen Cycle

MarinePure GEMS

MarinePure® biofilter media is a man-made ceramic. The unique combination of its vast surface area and open porosity with “Thin Bio-Film Technology™” allows for a healthy biofilm to develop. Due to its open pore structure, water can move easily throughout the entire media and consequently allowing the bacteria and its biofilm to have access to all nutrients and nitrogen compounds it needs to successfully colonize. Ammonia and nitrites are easily eliminated. Additionally, due to the nooks and crannies of the pore structure of MarinePure, anaerobic bacteria have a chance to develop in the inner structure of the media allowing for the reduction of nitrates.

Aquarium maintenance can be reduced because MarinePure biofilter media does not need to be regularly cleaned and water changes are reduced due to the lower nitrate levels achieved. MarinePure contributes to a more consistent water chemistry and allows for a higher fish load. Contact for more information. Cermedia LLC, located in Buffalo, NY manufactures MarinePure® Biofilter Media.


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