What is Biofiltration and How does it work in Aquariums?

August 5, 2020 Phil Overton

So, you have discovered the beautiful world of home aquariums and now you find yourself excited to begin your new journey with your own. Well, before you begin, you will need to have a clear understanding of how to take care of your aquarium and all the living organisms in it.

A Healthy Freshwater Aquarium

To properly run a successful aquarium, its essential for you to make sure the water has the correct living conditions for your fish to live in. These conditions go from having the correct water temperature to making sure the water is free from harmful toxins and chemicals. One of the key components of keeping your aquarium healthy is biofiltration. Here we will discuss what biofiltration is and how it works to keep your aquarium healthy and beautiful.

What is biofiltration?

Biofiltration is the process used to remove undesirable naturally occuring waste (ammonia NH4, nitrite NO2, and nitrate NO3) using living microorganisms that will modify the waste into less harmful substances. This process is called the Nitrogen Cycle. With the help of bacteria, this cycle converts ammonia into nitrite, then nitrite into nitrate and when the proper conditions are present, nitrate back into nitrogen gas.


The nitrogen cycle begins when fish are introduced into the aquarium. Fish waste from digestion and respiration, along with uneaten food and dying plant matter, break down into ammonia (NH4). Ammonia is highly toxic for fish. Even at low concentrations, it can severely stress the fish by basically burning the gills and interfering with the fish’s ability to use oxygen from the water. This damages the brain and organs of the fish, eventually causing it to die. However, once ammonia starts to develop in your aquarium, beneficial bacteria called Nitrosomonas and/or Nitrosococcus will naturally start developing. This can take 1 to 6 weeks for this bacteria to become established in an aquarium. These bacteria will convert ammonia into nitrite (NO2).

2NH3 + 3O2 → 2NO2 + 2H + 2H2O

Although less toxic than ammonia, nitrite will still harm your fish. Nitrite toxicity causes a weaker immune system, exposing your fish to diseases and bacterial infections. It also limits the ability of blood cells to carry oxygen, basically leading the fish to suffocate even when there is enough oxygen in the water. As nitrite rises in your aquarium, beneficial bacteria called Nitrobacter, Nitrospina, Nitrospira, and/or Nitrococcus will start colonizing and converting nitrites into nitrates.   This takes a week or two longer than the first step. The process of changing ammonia into nitrate is called nitrification.

2NO2 + O2 → 2NO3


Nitrates are not as harmful to your fish if kept in an acceptable level. However, at a high level, nitrates will still cause stress on your fish which leads to a weaker immune system, poor growth, damaged to their reproductive system, and a reduced life span.

One way to lower nitrates is to perform water changes

There are several ways to keep your nitrates levels low in your aquarium. You can do so by performing water changes, adding plants that consume nitrates (nitrates are a component in fertilizers), and by creating the right environment where denitrifying bacteria like Pseudomonas and Paracoccus can consume nitrates to turn them into nitrogen gas.  This last step usually occurs in a lower oxygen environment, typical of a media or rock with deep pores where the oxygen and be lowered during the nitrification process.

NO3 + CH2O + H → ½N2O + CO2 + 1½H2O

A properly established aquarium will have successfully completed the Nitrogen Cycle with nitrates consistently at and acceptable low level.

Biofilter media; How do they work?

One thing to keep in mind is that bacteria will grow and develop a biofilm on all available surface area in the aquarium. The total surface area ultimately determines the amount of bio load your aquarium can handle. If there isn’t enough surface area, the bacteria will compete with each other for the available space, building up the biofilm and causing the lower layers of the biofilm to die. Hence, the key for success in biofiltration is making sure you have ample surface area where the beneficial bacteria can grow and colonize without competing for space.

Typically, in an aquarium, sumps and filters will have a dedicated area for the biofilter media. The role of the biofilter media is to facilitate the successful colonization of good bacteria in your aquarium by increasing the available surface area. Biofilter media comes in all types of material from plastics, to sponges, naturally occurring rocks, and man-made ceramics and these all come in a variety of shapes.

The shape of the media is not as important as the porosity and the surface area it offers.  Open media (e.g. plastic) will have minimal surfaces and therefore the capacity it can offer is limited. Conversely, there are very high surface area media with very small porosity.  If the porosity is too small, water transport is inhibited, and the bacteria could actually be too large to fit in the pores.  There are media that are purposely shaped with a hole in the middle. Usually, the hole is added because the media is not porous enough for water transport and the hole increases the amount of available surface area in the media itself. (For more information on the relationship between material and surface area please read Are Bio Balls a “Nitrate Factory”? Plastic vs. Non Plastic Bio Filter Media: What is the Difference?

MarinePure Spheres, with High Useable Surface Area

No matter the size nor the composition of the media, the main questions to keep in mind are: How much more useable surface area will the media add? Will it be enough for your aquarium? Having the right media for your aquarium means that the media will provide more surface area than necessary. Therefore, in the case where there is an upset to the aquarium, the bio film and bacteria will have enough space to expand without competing for space and the media will not get clogged by its own biofilm growth.

Why is MarinePure® different and how will it help?

MarinePure® is a man-made ceramic biofilter media that has a combination of a large surface area and open porosity. This combination allows water to flow through the entire media, allowing for transport of the necessary nutrients to the bacteria. This unique feature allows bacteria to flourish throughout the entire media, thus utilizing all the available surface area. Which in turn, a thin, healthy biofilm is developed without the risk of plugging the media.

Due to its huge surface area, MarinePure can significantly reduce the amount of media needed to successfully run a healthy aquarium. In exchange, you will not need a large designated area for your biofilter media. In addition, due to MarinePure’s open porosity, you will not run the risk of having a clogged media that needs frequent maintenance nor have the need to replace the media. This is a very handy feature that will save you time and money in the long run.

MarinePure Block

Place MarinePure in an active or high flow area of your system to remove Ammonia and Nitrites. Because if its pore structure, MarinePure will still allow some areas in the media to be low in oxygen, thus promoting the colonization of denitrifying bacteria that will help complete the nitrogen cycle (or the conversion of nitrates to nitrogen gas). This allows for fewer water changes. However, if you would like to have even more control of Nitrates, then place MarinePure in a passive or low flow area, where water is allowed to travel around the media, and larger low oxygen zones can develop. MarinePure also comes in different shapes and sizes making it easier to use it in any type of aquariums and set up. 

If MarinePure intrigues you and you have any questions, please feel free to reach out to us. We would love to help you.

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Contact us to learn more about how MarinePure and BioVast can help your aquarium and aquaculture environments!


P.O. Box 600
66 River Rock Dr.
Buffalo, NY 14207

info@cermedia.com or

(716) 549-6600

Leyda Vazquez
Business Development Manager
(716) 549-6600 x264

Paul Pustulka
General Manager