Mechanical Filtration vs Bio-Filtration: Do You Need Both for Your Aquarium?

May 7, 2020 Phil Overton


When starting an aquarium, new hobbyists are often confused with the difference between what mechanical filters and biological filters do and whether both are needed. Since both filters have parts that have multiple functions, is it really necessary to have both? This article will explain the difference between mechanical and bio-filteration and which is best for your home aquarium so as you’re setting up your tank you will know which filter to include and why.

What is an aquarium mechanical filter?

Most hobbyists aim to have their aquarium water crystal clear. A clear, well-lit aquarium allows colors to pop and the tank to appear cleaner and healthier.

A mechanical aquarium filter goes a long way in making the water clear. The mechanical filter is an actual physical “screen” placed directly in the water flow. You can think of this filter as a strainer that will filter out particles that will cloud your tank. It is used to trap fish waste, food waste, floating algae, stirred-up sediment, dust and even bubbles. Removing these will help reduce tiny particles floating in the water that obscure water clarity.

Technology has changed in the past few years making it easier to find advanced aquarium filters. There are many unique and efficient filters available. These include hang-on-the-back filters and in-tank filters for smaller aquariums.

An aquarium filter: external hanging box filter.

An aquarium filter: internal box filter with a spray bar.

Larger tanks will use canister filters or even sumps, which are popular in saltwater aquariums. A sump is a large container, sometimes even another aquarium, hidden from view below the visible aquarium. Many other types of filtration and water control equipment can be placed in the sump.

An aquarium filter: external canister filter.

An aquarium sump with both mechanical in biological filtration, Plenty of room for other control components.

Nano tanks now come as all-in-ones, with filtration chambers hidden behind a partition wall in the back of the tank. These simple designs make it easy to set up an attractive aquarium in very little time

Each of these filters usually includes several components. There is always a pump (or air bubbler) and almost always, mechanical filtration. There is usually space for some bio-filtration and can include space for chemical treatment (i.e. carbon which help to adsorb some impurities and organics that will make the water smell bad).

The mechanical filtration is used to catch particles. This filter can be made from sponge, floss matting, plastic matting, packed sand, fine mesh bag and even cut nylons. The range of mechanical filtration materials is endless. See pictures below for some examples:

Over time, ranging from days to a week or two, the mechanical filter will accumulate particles and build up with material as it segregates the solid material from the system. It is usually easy (and necessary!) to clean or replace the mechanical filter media often. One reason is to prevent a buildup of material that may lower the pump flow rate. The other more important reason is to remove particulate organics which can chemically break down to ammonia. This leads us to bio-filters.

What is an aquarium bio-filter?

An aquarium bio-filter, by facilitating the growth of beneficial bacteria, works on the part of the chemistry of your aquarium known as the nitrogen cycle.  It often uses porous filter media to support this growth.  All fish waste, uneaten food and other protein-based wastes will break down into ammonia (even fish respiration produces ammonia), which, when accumulated in your tank, is very harmful to fish. Ammonia burns their gills and makes oxygen transport impossible.

Luckily, naturally occurring beneficial bacteria will grow on the bio-filtration media that then feed off the ammonia and convert it to nitrite and ultimately, nitrate. These bacteria typically grow in films (biofilms) on surfaces in the aquariums. The surfaces can be the tank walls, the hoses, plants and gravel. Even though these surfaces can host some biofilm, they usually will not provide enough surface area for biofilm to grow to significantly impact the nitrogen cycle, at least in the way your tank will likely need it to. That is the place for bio-filters. Bio-filters are designed to have large amounts of surface area for biofilms, and the nitrifying bacteria to grow, thus increasing the nitrifying capacity of the aquarium.

Plastic Bio-Balls

The material used in a bio-filter is called bio-filter media. They can range from homemade systems using scrunchies in a bucket, to sponge filters and plastic bio-balls in shower filters. They get more advanced, with much more surface and capacity with different forms of ceramic media, sand, natural stones, lava rock and even porous coral rock (live rock or dry rock). (For more information on this topic, see this blog article that discusses the difference between plastic and ceramic medias and the belief that plastic medias are “nitrate factories.”)                  

A planted tank will also have beneficial bacteria that will grow on the roots converting ammonia to nitrates, and the plants will also adsorb nitrates as a nutrient.

Planted tropical fresh water aquarium


Ceramic Noodles

The increase in surface area with these bio-medias can vary widely, along with their capacity, and their price. Some bio-medias require cleaning or replacement because the bio-load is high relative to their smaller surface area ceramic noodles, sponges, floss, and sand. If you do replace the older media, you are also getting rid of the beneficial bacteria your aquarium had developed.  (Please note, do not use chlorinated tap water to clean your media as the chlorine will kill off the beneficial bacteria population.)

Other bio-medias, including live rock and high surface­–area ceramic media such as MarinePure® Bio-Filter media, can be left alone in the system as the biofilm has more than enough room to grow and therefore does not clog the media.


MarinePure Spheres

The table below shows the amount of surface area available for some different medias, expressed as square meters of surface area per liter of biomedia:

Surface Area of Typical Bio-Filter Media

Media Name Type Surface Area (m2/l)
MarinePure® Spheres ceramic 435
Ceramic Noodles ceramic 93
Bio-Balls plastic 0.32
Dry Rock (reef) ceramic 132
Foam poly 0.82
Sintered Glass glass 270

To take it one step further, here is an interesting discussion on the surface areas in different medias—not all surface area is “useable.”  

Completion of the nitrogen cycle, lowering nitrates

After the beneficial bacteria complete the nitrifying process, nitrates are left in the tank. Fish and corals have a wide range of tolerances to nitrate, with some being very sensitive. There is a variety of problems that can occur with fish, including loss of appetite and equilibrium. Nitrates in coral tanks need to be low or their colors will be affected and growth diminished.

A Beautiful Reef aquariums

Nitrate reduction in an aquarium is more complicated than ammonia elimination, as the nitrate-reducing beneficial bacteria require a low-oxygen environment. Some bio-medias are completely exposed to oxygenated water, like plastic media, so the final stage of the nitrogen cycle (converting nitrates to nitrogen gas) does not occur.  Again, refer to this blog for a discussion about “nitrate factories” and the difference between plastic and ceramic medias.                  

There are a few methods other than bio-filtration to remove nitrates, the most common being water changes, which can be time consuming, and, especially for saltwater systems, costly. Meanwhile, ceramic media, live rock and deep sand beds have deeper sections where oxygen levels become lowered and the low-oxygen bacteria that complete the nitrogen cycle can do their job: reducing nitrates to nitrogen gas. Planted tanks will use the nitrates as a nutrient. (Note: Algae also will use nitrate as a nutrientwhich affect the clarity of the tank.)

Do you need both for your aquarium?

The answers is YES! Both filters are important, and although one is absolutely critical to keeping your fish healthy (bio-filtration), the other (mechanical) ultimately aids the function of the bio-filter.

A bio-filter is needed for the health of your aquarium inhabitants. A system with no bio-filter is just one step away from crashing. While the gravel and aquarium decorations might provide surface area for bacteria, any upset to the system (a dead fish, over feeding, etc.) will overwhelm available surface for the biofilm to spread, and ammonia levels will spike. A well-established bio-filter, with extra capacity, will keep the water parameters (ammonia, nitrite, and nitrate) stable and minimize issues.

Child watching fish tank. Aquarium with cichlids

Besides improving clarity, a mechanical filter does two things. First, is that it will provide some limited surface area for bio-films, helping with the overall nitrogen removing capacity of the entire system. More importantly, if it is cleaned regularly, the organic particles in the system (food, algae, fish poop) can be removed well before it is broken down into ammonia. Basically, by cleaning the mechanical filter regularity, total capacity of the system to handle nitrogen waste is increased. The results are a more stable, higher clarity, and healthier aquarium for you to enjoy.

Can Cermedia Help?

Cermedia LLC, located in Buffalo, NY, manufactures MarinePure® Bio-Filter Media. It is a man-made ceramic bio-filter media that has a huge amount of surface area for biofilm production in addition to a large network of open porosity. These features enable water to move easily throughout the part, allowing the nitrogen components to find the bacteria for conversion, allowing all parts of the nitrogen cycle to take place, including ammonia and nitrite elimination and nitrate reduction. Marinepure also does not need to be cleaned, there will always be open pores, as long as there is mechanical filtration pulling out the large particles before they encounter the MarinePure bio-filter media.

MarinePure GEMS

If you have any questions about how to access MarinePure® Bio-Filter Media or incorporate into your new or current tank, feel free to reach out to us. We’d love to help walk you through how to use this bio-filter media for a cleaner, easier-to-manage fish tank.

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