Reef Aquarium Filter Types

Reef Aquarium Filter Types 101 Guide

Reef Aquarium Methods of Filtration

You decided which type of aquarium you wanted and have probably spent way too much money procuring it. Now it’s time to pack it full of corals, fish and other aquatic goodies, right? Wrong!

You haven’t planned your filtration system yet. If you pack the tank full of inhabitants without a proper filtration system, they will all be poisoned by their own by-products and die!! I know that reads pretty harshly, but it’s the truth. Without adequate filtration and a fully cycled aquarium, your construction efforts will only lead to disappointment, dead corals and a drained checking account.

Every living creature that you will eventually place in your aquarium will produce ammonia, just like humans do. If the ammonia is not removed quickly and efficiently, the aquarium inhabitants will be poisoned and, in due course, die.

There are three types of filtration used in a reef aquarium: Mechanical, Chemical and Biological. Each method approaches filtration in a different manner though they all accomplish the same task, tank filtration that maintains an ideal environment for your aquariums inhabitants. Please follow the links below to educate yourself on the specifics of each filtration type and determine which type of filtration system would be best for you, your tank and its inhabitants:

Reef Aquarium Filters – Chemical Filtration Explained

Reef Aquarium Chemical Filtration Overview

Chemical filtration is defined as using any medium that alters the composition of the substance it is placed in. This means that when a chemical filtration medium is placed into an aquarium, it changes the composition of the water by removing dissolved organics, toxic metals, chloramines, enzymes and gasses. There are many types of chemical filtration medium used in marine and reef aquariums. The most widely used media are listed and explained below for easy reference.

Activated Carbon For Reef Aquarium Filtration:

By far, the most common method of chemical filtration in the marine and reef aquariums is the use of activated carbon. Activated carbon is manufactured by exposing coal carbon to high heat and steam which creates a micro-porous material. Microscopic pores absorb heavy metals and organic molecules by trapping the molecules through a process know as molecular sieving. The highest quality activated carbon is made from coconut shell and is the type recommended for reef aquariums. The best activated carbon will be low in ash and will float and fizz when initially exposed to water.

In recent years there has been a large amount of discussion on the possibility of activated carbon leaching dangerous levels of phosphate into reef and marine aquariums. Indeed, activated carbon does leach phosphate as it is being used in an aquarium, but not at dangerous levels. Activated carbon leaches a non-toxic amount of phosphate because it is made from coal which was once plant matter, and plant matter contains a high level of phosphate.

It’s important that you only purchase high quality activated carbon that has been acid washed prior to packaging in order to reduce the amount of ash on the carbon. It has been found that activated carbon with higher ash content leaches more phosphate into the water than those with a low ash content. Yes, this means you should use the expensive carbon (relatively speaking).

It has also been said that activated carbon removes trace elements needed by corals in reef aquariums. Yes, activated carbon will remove an amount of trace elements from the aquarium water, but in essence, that’s its job (to remove dissolved elements from the water). The amounts of trace elements that are removed are easily replaced by using a supplement like Kent Marine Trace Elements. The pros of removing the dissolved organics and heavy metals far outweigh the cons of losing trace elements that can easily be replaced. We recommend using activated carbon to maintain a clean, odorless and colorless aquarium while dosing it with a high quality trace element supplement to replenish those lost by using the carbon.

The amount of activated carbon to use varies with the use of the aquarium, but as a general starting point we recommend about ? cup for each 20 gallons of water, replaced every 6 weeks. You must make sure to thoroughly wash the carbon before use in order to remove as much ash as possible. When washing, place the carbon in a filter bag and rinse until the water running off of the bag is clear. If you massage the carbon you will create more ash, so just rinse without disturbing the particles and use when the water runs clear.

Phosphate Removers For Reef Aquarium Filtration:


Phosphate removers include Aluminum and Iron Oxide granules. It has been found that Aluminum Oxide will leach aluminum into the aquarium and has since been phased out with the advance of Iron Oxide. Iron oxide is a mineral that has the property of absorbing phosphate and other materials into its porous structure by means of ion attachment. This type of chemical filtration is best used when water is flowing through the medium at a slow rate, so a phosphate reactor is often used.

A phosphate reactor is just a canister that houses the phosphate removal medium and allows it to tumble as a power head slowly circulates water through it. There are many different manufacturers of phosphate removal medium and each medium should be used per the manufacturer’s directions. Such removers are very useful materials in the reef aquarium, and when a developed reef has been established, it is almost mandatory to use some sort of phosphate remover. The levels of phosphate in the reef aquarium should always be kept below .7 ppm, but if you are planning on having small polyp stonies (SPS’s) in your aquarium, levels below .3 ppm are mandatory and levels of 0 ppm are ideal.

Nitrate Removers For Reef Aquarium Filtration:

Nitrate removers are very porous material that resemble crushed coral or gravel and work by increasing the levels of natural anaerobic de-nitrification in the aquarium. These products accomplish this task by being impregnated with anaerobic bacteria that naturally dissolve nitrate.

The same thing that is accomplished while using a nitrate remover happens constantly when a reef has an incorporated Refugium (which we’ll be discussing later). Anaerobic de-nitrification occurs best when exposed to low levels of oxygen; this is why refugiums have a deep sand bed. Thus, nitrate removal mediums should be positioned in an area with low flow rates. Levels of nitrate should never exceed 10-15 ppm, but ideally, a level of below 5 ppm should be maintained.

Poly Filters For Reef Aquarium Filtration:

Poly filters are sponges, cloths or other materials that have been impregnated with one of the materials previously listed (activated carbon, iron oxide, etc.) or another chemical material. The main selling point for this type of filter is convenience. They are often marketed as “cut to fit your filter” or “only use as much as you need.” These filters are actually just sponges laced with the by-product (dust) of one or more of the manufactured materials above – a phosphate removal poly filter is a sponge with Iron Oxide dust impregnated into it; a carbon poly filter is a sponge with carbon dust impregnated in it, and so on.

These types of filters are not recommended by as you can never know exactly how much active product you are using, and you will always spend more money on this type of filter due to the additional manufacturing processes needed to create it.

Reef Aquarium Filters – Biological Filtration Explained

Reef Aquarium Biological Filtration Overview

Biological Filtration is the removal of nitrogen breakdown by-products (Ammonia, Nitrite, Nitrates, etc.) from the aquarium water through the use of bacteria.

Nitrogen compounds appear as a result of animals and food being added to the tank, algae dying within the tank, and the respiration and metabolism of the fish and invertebrates in the tank. The water quality of your aquarium will start to deteriorate quickly with the addition of more animals; however, biological filters can counteract this negative effect by removing the organically produced toxic compounds. Biological filtration is often executed with live rock, live sand, or bio-balls placed in a wet-dry filter.

Biological filtration is used to (1) remove nitrogen breakdown by-products, (2) convert ammonia to nitrite, (3) convert nitrite to nitrate, and (4) remove some nitrate from the system. To do this, bacteria is used to eliminate ammonia, nitrite and nitrates. Ammonia is broken down to nitrite by a form of bacteria known as Nitrosomonas. These bacteria can appear spontaneously or proliferate when adding/transferring gravel or rock. Ammonia tests should always show zero ppm; even small amounts of ammonia are unacceptable in reef systems because they will easily harm your aquarium’s inhabitants.

Nitrobacter bacteria also appear spontaneously in aquariums and convert the nitrite to nitrate, a less damaging compound. If nitrite tests show the mere presence of nitrite, your tank must be thoroughly cleaned. You’ll have to remove any sitting organic matter and dead or dying algae. You’ll need to flush the mechanical filters, sift the gravel, check the corner overflow boxes and skimming siphons, etc. The presence of nitrite may be directly related to the presence of too much fish food or the tank being overloaded with life forms. Whatever the reason, your filters aren’t being able to efficiently deal with the biological load present in your aquarium. In accordance to the cause, you may have to remove life forms or add additional biological filtration.

Nitrates are different than ammonia and nitrite. Nitrate is not notably harmful to all-fish aquariums, but it is to reef aquariums. Nitrates directly affect the well-being and aesthetics of corals and other invertebrates. When testing your nitrate level, the lower the better; anything under 10ppm is satisfactory but in very sensitive reef aquarium a level of 1-4ppm is desirable.

Reef Aquarium Filters – Mechanical Filtration Explained

Reef Aquarium Mechanical Filtration Overview

Mechanical Filtration is the process of removing solid particles from aquarium water by some method of straining. This is mostly accomplished in the reef aquarium by a pre-filter on the overflow of the tank or by filter floss in the sump or wet-dry filter. Although mechanical filtration does not remove ammonia, nitrite or nitrate directly, it can remove the contributors to these compounds (i.e. biological waste, un-used food).

Fine and coarse foam, filter bags and filter floss are the most common types of material used in the reef aquarium to accomplish mechanical filtration. For easy reference, we have separated the filter materials below in a list to explain each of them and how they might be used.

Foam Filters For Reef Aquarium Filtration:

In a reef aquarium, you will almost certainly see a cylindrical foam filter on the overflow of the tank as well as one or more somewhere in the sump, refugium or wet-dry filter. The idea is to filter out any solid material from the water before it reaches the biological or chemical filtration media. As the biological and chemical filtration media works to remove organic and chemical compounds on a microscopic scale, dumping large amounts of coarse material would only clog the filters and reduce their efficiency.

Foam filters come in a variety of densities which give each of them different properties. Coarse foam filters strain out large pieces of material and tend to clog at a slower rate than fine foam filters. The coarse foam works well as a pre-filter, catching large pieces of food and waste material; however, it falls short if needed to filter fine material.

Filter Bags For Reef Aquarium Filtration:

Filter bags are mostly used in refugiums as pre-filters, but they can be used in any application where there is a place to mount them. The point is, as the name states, to have a porous material in the shape of a bag that can be fitted to piping and provide filtration “from the inside out.”

The perfect application for a bag filter is where an overflow enters a sump, refugium or wet-dry filter. A bag filter can be fitted over the overflow pipe to catch material before it moves into the biological or chemical filtration media. Bag filters come with smaller mesh than most other filter types, so they must be cleaned often.

Filter Floss For Reef Aquarium Filtration:

Filter floss comes in sheets that are sometimes called filter pads. They come in various densities, thicknesses and colors. The most common form of this media is the multi- density pad which is used in wet/dry filters before the water trickles onto the bio-balls. This pad usually comes in white and blue coloration as the different colors represent varying densities of the floss. The white floss is very coarse and, thus, traps larger pieces of material whereas the blue fiber is very dense and filters out finer pieces of material. When you use multi-density floss, be sure to put the less dense material upstream of the denser to aid in even dispersion of the water, preventing premature material clogging.

Reef Aquarium Filters – Using a Refugium Filter

Refugiums For Your Reef Aquarium

The refugium system is my favorite and is the system type I use on all of my reef aquariums. This type of system is based on the sump type system and starts with a separate aquarium that will house all the components and increase overall water volume.

To create a refugium system, you place live rock, a large amount of macro algae, and a deep sand bed inside your sump. The sand bed replaces the need for bio-balls or any other type of biological filtration. The benefits of having a refugium on your aquarium are as follow:

1) The increased water volume will create all of the benefits that were listed in the sump filter section.

2) The removal of bio-balls and the addition of live rock have a two-fold effect… First, do you remember that the bio-balls would release Nitrates back into your aquarium water? Well, eliminating bio-balls will eliminate that potential problem. Second, the addition of live rock creates a bacteria rich environment that will increase the transformation of ammonia to less dangerous compounds.

3) The deep sand bed (at least 6” deep unless you’re using a refugium mud like “miracle mud”) will create a low oxygen environment that is perfect for the growth of nitrifying bacteria. These bacteria remove nitrates from the water and release them as nitrogen gas that is easily transferred to the air without additional equipment. These bacteria only exist in low flow, low oxygen environments and are the only way to remove nitrates from your aquarium without adding some type of chemical based nitrate remover.

Note: It is important that you do not disturb the refugium’s sand bed once your system is set up. When you create a low flow, low oxygen environment, hydrogen sulfide is created. This is a toxic compound that is very dangerous to aquarium inhabitants and it is essential that you do not disrupt it into your aquarium water. It might seem strange to have this type of system when it actually creates a dangerous compound, but when the refugium is established there will be no need to disturb the sand bed. Thus, hydrogen sulfide will never be released into your aquarium.

4) The macro algae that are grown and harvested in the refugium use the phosphate in the water as a fertilizer and, thus, lower your phosphate levels significantly. I had phosphate levels of .2 in my 65 gallon tank before I installed a refugium. Once it was installed, my phosphates were below .02!! When your phosphates are low, coralline algae will flourish, slime algae will die, and everything will be healthier.

5) A refugium must be lit 24 hours a day and, thus, will reduce if not eliminate PH drops at night.

6) A refugium will breed micro algae and copepods which will be pumped into your tank all day every day. The micro algae will feed your corals and the copepods will feed other reef inhabitants, especially Mandarin Gobies!! Even if the copepods get chopped up in the supply pump, their pieces will become healthy food for all of your reef inhabitants.

We recommend you put a refugium on your reef aquarium, period. This filter will complete your nitrogen cycle, stabilize PH fluctuation, reduce phosphate levels, breed beneficial copepods and micro algae all while increasing the volume of your aquarium system

Reef Aquarium Filters – Using a Sump Filter

Sumps For Your Reef Aquarium

An aquarium sump is simply another tank of water that houses various forms of mechanical, chemical and biological filtration. The benefits of having a sump on your aquarium are as follow:

1) A sump will increase the overall water volume of the system, leading to a greater stability of water parameters (including PH, salinity, Carbonate Hardness and Calcium levels). The larger water volume will also be more forgiving if an inhabitant dies, a dangerous chemical is dropped into the tank, or if your chiller/heater breaks resulting in a temperature change. Basically, with larger water volume in an aquarium, changes occur more slowly, thus giving you time to remedy any problem before it becomes a serious issue.

2) A sump provides ample space for all three types of filtration methods. Personally, I have a 20 gallon sump tank (refugium) attached to my 65 gallon reef aquarium. The flow in set up in my reef tank so that the water from my overflow goes directly through my protein skimmer. The water then flows through the refugium section where it flows over a wall into the pump section. The pump section houses my Phosphate remover, my activated Carbon, and my Mag Drive 5 water pump. All these things fit out of sight under my aquarium and there is still space available to add additional equipment if needed.

Although there are noteworthy advantages to having a sump filter system on a reef aquarium, there are also a few disadvantages and limitations with this system. The disadvantages and limitations of having a sump filter on your aquarium are as follow:

1) A sump requires additional room. To house your sump filter, you will need either a large enough area under you aquarium to place it or a way to pipe it so that it could be placed elsewhere. I know plenty of people that choose to have their sumps to the side or even across the room from their reef aquarium, but the extra piping might be too much for the novice hobbyist to tackle.

2) A limitation to the sump system correlates to the size of the aquarium it will be attached to. For example, it would be unnecessary to place a 10 gallon sump on a nano reef that is less than 15 gallons. The nano tank will most likely come with some sort of internal filtering system that is more than sufficient for filtering the water. I have, however, seen people that have large reef systems piped in series with other smaller tanks. With this design, they have a large display tank with one or more frag tanks, refugiums, or breeder tanks all piped with the same water.

Reef Aquarium Filters – Using a Wet-Dry Filter

Wet-Dry Filters For Your Reef Aquarium

The Wet-Dry/Trickle Filter is one of the most recognizable filters in the marine aquarium hobby. This filter is the one that your local fish store will try to sell you if you request a saltwater tank filter. The reason they are popular with the novice hobbyist is that they come pre-made; all you have to do is open the packaging and install it. These pre-made units come with an overflow box, a built-in protein skimmer, a tray with holes in it where the filter pad goes, as many bio-balls as the filter can hold, and a foam post filter. The only thing you need to add is a pump sufficiently large enough for the aquarium.

These filters have fallen out of favor with reef aquarium hobbyist because the bio-balls leach Nitrates into the aquarium water. The protein skimmers found on these types of filters are not very efficient either, and when used in a reef aquarium, they do not remove organics fast enough to keep phosphates and Nitrates at the levels they need to be.

These filters are very efficient at removing ammonia from the water and, thus, are a good option if you’re creating a fish-only aquarium. One problem with wet-dry/trickle filters occurs during their transformation of ammonia to Nitrite and then to Nitrate. In a reef aquarium, these compounds are dangerous to the sensitive corals and invertebrates and, thus, must be removed. However, the wet-dry filter is not capable of completing the nitrogen cycle and, in fact, adds to the Nitrate load of the tank.

We do not recommend using these filters for reef aquariums.

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