Filtration Basics

In my previous columns, I was in the process of creating a checklist for setting up a reef aquarium.In order to continue, it is important to have an understanding of aquarium filtration so that the most appropriate filtration method can be chosen.In this column, I will define the three types of filtration available to marine aquarists.


“Reef aquarium filtration.” These three simple words comprise one of the most controversial subjects among reef aquarists, ranking second only to lighting discussions.  The reason that this is such a controversial subject is because there are so many different filtration systems with which reef hobbyists can be successful.

Many different modes of filtration including biological, mechanical, and chemical filtration, as well as various combinations thereof exist, for reef aquaria. While all forms of filtration can help with the success of a reef aquarium, biological filtration is the most essential to the life and health of our aquarium inhabitants. In an aquarium, we need to make sure that we have enough biological filtration available to eliminate the amount of waste created by the inhabitants and chemical processes that take place.

Biological Filtration in Simple Terms

Biological filtration is a process that uses living organisms to change one form of waste (ammonia) into another. The breakdown of one of the more toxic forms, ammonia, into a less toxic form, such as ions of either nitrite or nitrate, is critical to the survival of our aquariums.

The following discussion of the filtration types and components is largely based on the in-depth discussion in “The Aquarium Reference – Systems and Invertebrates” by Martin A. Moe, Jr., 1992.


Although toxins may come in many forms, or can be airborne or introduced by contaminants, ammonia is perhaps the most important. Toxic ammonia accumulates in the aquarium from the breakdown of fish waste, decaying food, or other organic material. Additionally, ammonia is the major component of most marine animal urine. Ammonia can cause damage to fish tissue, disrupt the oxygen levels in the bloodstream and cause stress that can bring on disease or animal death.It is toxic to most marine life so there must be a way to eliminate or neutralize it in the aquarium water.This is where the bacteria that are part of our biological filter come into play.The process called “cycling” refers to the establishment of bacterial colonies in the filter bed that convert ammonia to nitrite and then nitrite to nitrate.After an aquarium has completed its cycle, the bacteria will have colonized the substrate (surfaces such as rock, sand and even glass) in the aquarium, and animal life can then be supported.

The bacteria responsible for the initial step of the nitrification cycles in our aquariums, consuming ammonia and converting it into nitrite, consist of various species from the following genera Nitrosomonas, Nitrosospira, Nitrosococcus and Nitrosolobus and others.These nitrifying bacteria are aerobic, which means that they need oxygen to survive. In an aquarium with good water flow, these bacteria will colonize all suitable aerobic surfaces within which the water comes in contact.

The next group of bacteria involved in the nitrification cycle is responsible for converting the previously discussed nitrite breakdown product into nitrate. This is accomplished by numerous bacterial species from the genera Nitrobacter, Nitrosospira, Nitrocystis, Nitrococcus and others.Nitrites are also toxic to many forms of aquatic life and can inhibit oxygen uptake in the bloodstream of fish.Fortunately, these bacteria keep nitrite at low levels in a fully cycled aquarium.

While nitrate is less harmful to our animals than ammonia or nitrite, it may cause excessive algae problems that affect the health of our animals.Algae require nitrate as a basic nutrient.If nitrate is allowed to accumulate in our reef aquariums in amounts above 5 ppm, it can affect the health of the corals that we are keeping by polluting the water and stimulating algal overgrowth of coral tissues.This waste product, the end product of the nitrification cycle, may be removed by such means as water changes, chemical adsorption, protein skimming, uptake by algae filtration or other organisms that can utilize nitrate as a dissolved nutrient source.


Since I am discussing bacteria, I will also mention some of the many forms of denitrifying bacteria found in our aquariums: Micrococcus, Pseudomonas, Denitrobacillas, Bacillus and others.Some of these are anaerobic (requiring little or no oxygen) and some are aerobic.The bacterial genus, Thiobacillus, consists of eight species.These particular bacteria utilize organic sulfur compounds such as sulfide, thiosulfate and bisulfite in low oxygen areas as a substrate to reduce nitrate in our aquariums.The bacteria consume the nitrate and convert it to nitrogen gas, which gets released into the air through water movement and aeration.Some suitable substrates for these bacteria are in the low oxygen areas in the center of porous live rock or in the deeper layers of a sand bed.

To briefly summarize this discussion of the Nitrogen cycle, please refer to the following diagram.


Now That We Have These Bacteria, Where Do We Put Them?

Nitrifying bacteria require a place to colonize and multiply in order for them to be efficient in converting waste (nitrogen compounds) in the aquarium.The media or substrate for colonization can consist of sand, rock, or man-made products such as bio-balls or other filter media.Since the main interest of a reefkeeper is a successful reef aquarium, using more natural forms of substrate is desirable.Our animals come from an ocean containing both live rock and live sand, and using natural forms of filtration will more closely mimic their original environment.Natural forms of substrate consist of live rock and live sand that will make up the foundation of the biological filter. On a side note, coral surfaces are also an excellent substrate for bacterial colonization.

Live Rock 

Live rock consists of calcium based coral skeletons that are populated with microscopic bacteria and marine organisms.Because live rock has a porous texture, there is a large, aerobic surface area for the microscopic nitrifying bacteria to colonize.Another property of live rock is its ability to provide areas where denitrification may occur.Below the aerobic surfaces of live rock are areas of very low oxygen that are suitable for beneficial denitrifying bacteria to colonize.

Live Sand 

Live sand consists of sand collected from the ocean that is populated with microscopic bacteria and marine microorganisms.Non-living sand can also be populated with bacteria and organisms that will convert it to live sand.In addition to numerous benefits for an aquarium to be discussed in a future article, sand is an excellent substrate for nitrifying bacteria.Typically, the sand surface area covering the bottom of an aquarium is very large, allowing it to perform as an effective biological filter.Like live rock, sand also works as an excellent denitrification filter when a bed of four or more inches of sand is used.Sand is so efficient that denitrification can even occur on a single grain of sand.

Chemical Filtration

Chemical filtration is the process of using organic or synthetic compounds to remove impurities from the aquarium water.Two of the more common forms of chemical filtration are granular activated carbon and molecular adsorption filters. 

Granular Activated Carbon (GAC)

While GAC is normally categorized under chemical filtration, it also has some mechanical filtration (see below) properties.Granular activated carbon acts as an organic sponge.The carbon is very porous, allowing it to trap physical particles.The process of trapping the waste particles is called absorption.There are also chemical properties that make carbon attract certain forms of impurities such as phosphate, organic acids, proteins, metals such as copper, and antibiotic compounds contained in the aquarium water.The process of attracting these impurities is called adsorption.One of the best uses that I have found for carbon is the removal of organic acids that give the aquarium water the yellow tint that is often seen by reef hobbyists.

Absorption is a process that works similarly to a sponge.The process can be compared to washing your car with a sponge.The car is sprayed with water, the sponge is then run over the surface, it collects dirt but leaves the water behind.Similarly, in the aquarium, water is forced through a medium (GAC) that traps waste particles; removing the medium brings the trapped particles along with it.

Adsorption is defined in Webster’s Dictionary as the capability of a solid substance (adsorbent) to attract to its surface molecules of a gas or solution (adsorbate) with which it is in contact.In our aquarium realm, the definition is the capability of a solid substance (carbon) to attract to its surface, molecules of a solution (aquarium water with impurities) with which it is in contact.

Adsorption may be analogous to the example of static electricity buildup on a computer monitor.The static electricity buildup on a computer monitor attracts dust particles from the air similar to how carbon attracts impurities from our aquarium water.The aquarium water (air) flows through the carbon (static charged computer screen), which attracts the chemical impurities (dust), binds them, and keeps them from going back into the aquarium water.Unlike absorption, which physically traps particulate matter, the process of adsorption chemically attracts impurities and binds them through chemical processes.

An interesting property of GAC is that it can be produced to remove specific chemical forms of waste or contaminants from the aquarium water.By producing GAC at different temperatures, sizes, and textures, or by adding certain chemical elements, it can selectively remove impurities.

GAC may be used in different ways:It can be placed in a canister filter so that all water drawn through the filter passes through it for maximum contact time.It can also be used passively by being placed behind rockwork or in a sump where water flows around and through it.While forcing water through GAC is thought to be the most efficient usage of absorption and adsorption, it will still work well if used passively, primarily due to its adsorption properties.

Molecular Adsorption Filters

Molecular adsorption filters such as a PolyFilter™ from Poly-Bio-Marine work similarly to carbon by using chemical bonding to attract impurities or excess nutrients from aquarium water.Depending upon their composition, they can be made specifically to remove toxins such as copper and other metals, or even excess nutrients such as phosphate.This type of filtration is normally used for short periods of time, and is best suited for quick removal of excess organic waste or toxins that may have been accidentally introduced into the water.While they can be used for longer periods of time, it is better to find the source of the problem rather than relying on an absorption filter to remove chronically problematic levels of certain substances.

Mechanical Filtration

The primary function of mechanical filtration is to remove large particulate matter from the water before it begins to decompose.Filter sponges, polyester floss, and micron filters are some of the more common forms of mechanical filtration media.While mechanical filtration can be used on a reef aquarium, it may become a detriment if not used properly.If the mechanical filter media is not cleaned often, the particulate matter trapped by the filter will decompose and pollute the aquarium water. There are times, however, when a mechanical filter can be used to quickly remove large particulate matter from the water.Removing unsettled sand from a new aquarium or when a large amount of particulate matter is introduced (e.g. disturbing a sand bed or live rock), are events when mechanical filters can be beneficial.

Protein Skimming

Protein skimming is one of the more popular and effective forms of filtration.An advantage of protein skimming is the ability to remove organics and waste material from the aquarium before they begin to be broken down by the biological filter. 

The process of skimming involves the following: 

· Water and large amounts of air are injected in to a columnar shaped device.
· The air and saltwater are forcefully mixed together, creating bubbles.
· The bubbles become coated with organics and proteins (adsorption), creating foam (or skimmate.)
· The foam rises up the column into a collection cup, located outside of the aquarium, where the organics and proteins are removed from the water.

Another advantage to protein skimming in the reef aquarium is that the mixture of air into the saltwater increases the amount of oxygen in the water, which, in turn, is beneficial to the health of the aquarium inhabitants.

An in depth explanation of protein skimming is available in a Reefkeeping feature article by Frank Marini located here.


Summing up, I have explained the three basic types of aquarium filtration: biological filtration is required to maintain life in our aquarium; chemical filtration can be a useful aid in removing impurities from our aquarium; and mechanical filtration such as protein skimming can help in continuous waste removal while other forms of mechanical filtration can aid in the removal of large particulate matter under special circumstances. Additionally, there are others forms of filtration that I will discuss in a future article.

If you have any questions about this article, please visit my author forum on Reef Central.


Very special thanks to Eric Borneman for his Olympian efforts assisting me with this article and providing the graph on the nitrogen cycle.

References Cited:

Moe Jr., M. A. 1992. The Aquarium Reference – Systems and Invertebrates. Green Turtle Publications. Plantation. pp170-178.

Reefkeeping Magazine™ Reef Central, LLC-Copyright © 2008

Filtration Basics by Doug Wojtczak -