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Biological Filtration for Aquariums: How It Works

Maintaining adequate biological filtration for aquariums is a major part of good fish health. When your biological capacity suffers you’ll see fish diseases take hold, water chemistry go awry, and even deaths if not immediately corrected.

If you’ve ever wondered what’s going on under the hood of your filter now’s a good time to get to know biological filtration!

What is Biological Filtration?

Aquarium filters have a very specific job: removing harmful agents from the water. These agents can vary quite a bit depending on what sort of animals and plants you’re keeping.

However most filters are designed to remove nitrogenous wastes (ammonia, nitrite, nitrate, and proteins), organic molecules, and particulates (leftover food, detritus, etc). In order to do so these filters use three distinct types of filtration: chemical, mechanical, and biological filtration.

Chemical filtration is exactly what it sounds like: using agents to absorb or chemically alter components in the water column. Activated carbon is used in most filters for this purpose as it can attract organic molecules to itself and hold them until either bacteria digest them or you replace the carbon.

Other forms of chemical filtration include ammonia absorbing resins and chemical additives that neutralize heavy metals.

Mechanical filtration involves using physical barriers like filter floss to screen out particles from the water. Sponge filters rely heavily on mechanical filtration, for example.

Biological filtration is the third and most essential type. Here we rely on beneficial bacteria to break down waste products into harmless forms. Biological filtration is thus an extension of the aquarium ecosystem and very important to understand.

Getting to Know Bacteria

While germs have a bad reputation they are actually essential for biological filtration in aquariums. Without them nitrogen byproducts would quickly build to lethal concentrations, killing off fish and allowing algae to take over. Fortunately, there are two groups of bacteria that help keep fish alive and algae growth in check.

Nitrifying Bacteria

Ammonia is the agent that causes the most harm in the Nitrogen Cycle. It’s excreted by fish and is a common product of organic decomposition. Nitrifying bacteria are useful because they use it as food!

Germs of the genus Nitrosomonas take ammonia and convert it into nitrite. Now, nitrite is less toxic than ammonia but still a problem agent. Fortunately, Nitrobacter and Nitrospira bacteria are present in a well cycled aquarium, which eat nitrite and convert it into nitrate.

All of these organisms are aerobic, meaning they require oxygen to survive, much like fish and humans. Fortunately, they exist in the millions throughout the ecosystem.

New aquariums don’t have any of these bacteria, making them susceptible to New Tank Syndrome. How they get there is a matter of chance and Nature’s whim since Nitrifying bacteria don’t form spores: the hardy “shell” that lets many microorganisms survive dormant for years.

They do exist in the air, soil, water, and are carried into your house and aquarium as you enter and leave. Nitrifying bacteria also get a chance to spread when you introduce your first fish and plants. They live on the surface of plants and in the water column of the established aquarium, helping jump-start your new ecosystem!

Denitrifying Bacteria

Nitrates are the “final” step in the Nitrogen Cycle as it is usually presented. And since it’s the least toxic compound in the chain it usually builds up slightly, only to be removed through regular water changes.

Nitrate is not harmless, however. Concentrations greater than 50ppm result in Nitrate poisoning. Symptoms include brown gills, gasping at the surface or near areas of swift current, and listlessness.

While nitrifying bacteria are obviously essential there’s a secondary class of organisms that are often overlooked: denitrifying bacteria. These microorganisms have an odd quirk, however: they are anaerobic, meaning they don’t use oxygen to breathe. In fact, O2 in concentrations greater than 10% are poisonous to them!

This means they can’t survive alongside nitrifying bacteria in typical places, like most biomedia, filter mesh, gravel, etc. Denitrifying bacteria live in the areas where oxygen is scarce: sand substrates with slow water circulation and within the deeper pores of rocks and ceramic biomedia.

They convert Nitrates into Nitrogen gas (N2) which simply outgasses back into the atmosphere. Since Nitrates are rarely allowed to build up denitrifying bacteria don’t get much attention in freshwater setups.

However marine organisms and invertebrates of all types are especially sensitive to nitrate, making complete biological filtration essential to their well being.

Best Tools and Media to Enhance Biological Filtration

Here are some of the best tools on the market to enhance the biological filtration capacity of your aquarium.

Ceramic Biomedia

Ceramic biomedia is the best addition for most filters because they provide a massive amount of surface area for nitrifying bacteria to colonize. The open cylindrical design helps water to flow freely through the media, ensuring a thorough mixing and removal of ammonia and nitrites.

However most ceramic media on the market has pores suitable for aerobic nitrifying bacteria. This means your media will reduce ammonia down to nitrate and no further. As long as you’re doing regular water changes this isn’t really an issue.

However the free flow of water means anaerobic (oxygen-hating) denitrifying bacteria don’t have a home as they’ll be constantly poisoned by O2.

Seachem Purigen is a brilliant product for this reason. The pores are designed in order to allow nitrifying bacteria to colonize the surface but denitrifying bacteria to thrive within each nugget, safe from the ravages of oxygen. This makes it especially suitable for saltwater and invertebrate setups where nitrate concentrations are critical to keep down.

Seachem Purigen Organic Filtration Resin - Fresh and Saltwater 250ml
  • FILTRATION: Purigen ranges in color from almost...
  • SELECTIVITY: Seachem Purigen is an organic...
  • CAPACITY: Being both spherical and macroreticular,...

Cycling Bacteria

Cycling has come a long way from the fishless ammonia and add fish and wait days. Now you can simply buy bottled Nitrifying bacteria to add right to your aquarium.

Beware products that require refrigeration as these contain live bacteria that may end up consuming all of their food and simply dying before being added to the tank. Fluval Cycle Biological Booster‘s bacteria are dormant and can be kept at room temperature without issue.

Fluval Cycle Biological Enhancer, Aquarium Water Treatment, 16.9 Oz., A8351
  • All-natural water care creates a safe biological...
  • Infused with a powerful team of beneficial...
  • Extremely effective when setting up a new aquarium...

Bottles of Nitrifying bacteria can also be added if you suffer an ammonia spike after using an antibiotic or an aquarium spring cleaning removes too many microorganisms!


Biological filtration happens whether you understand the process or not. But knowing how it functions ensures you can provide optimal conditions for proper waste removal. If you’re interested in learning more about how to seed and maintain a good environment for bacteria, have a look at my guide on How to Speed Up the Aquarium Nitrogen Cycle!

Jason Roberts
About Jason Roberts
Jason is an aquarium fanatic that has been a fish hobbyist for almost three decades.

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