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Filtration systems are the backbone of our saltwater aquariums. Without some method of breaking down waste produced by the organisms in our aquariums, our fish and invertebrates would end up, for lack of a better term, living in a cesspool of their own waste.

Our #1 priority as aquarists is to provide the highest quality water we can for our wet friends to live in.

In this article, I will talk about the different methods of filtration available and what type of tanks they are suitable for, along with some of the most popular types of filter media to help maintain the best water quality in your own aquarium.

In an article I had written last year called “Things to know before buying an aquarium filter”, I discussed some of the things a filter system can do for you, four of the most popular filter systems and some items to consider before purchasing a filter. This article is a good starting point if you are not too familiar with the different types of filters out there and the advantages of each.

The article doesn’t, however, break down which filter systems are best for certain aquarium types and that is something we will address in this article as well as touch on the most popular types of filter media.


Let’s start with talking about filtering a reef tank. The big question many people have: Is there one “best” way to setup a filter system for a reef tank? The simple answer is “No, there are many different ways to filter a reef tank and they can all work very well”. But one thing 99% of all reef tanks have in common is the use of live rock (covers the biological needs in a reef tank) and a protein skimmer (covers the mechanical needs in a reef tank).

Live rock is rock that has been harvested from the ocean in tropical locations such as Fiji, Tonga and the Marshall Islands. The rock is very porous and will act as a biological filter for your tank as it will contain beneficial bacteria to help breakdown fish waste. People will disagree on how much rock to use in a reef tank, but generally it is recommended to use anywhere between ½ to 2 pounds per gallon of water. Live rock must also be properly cured before any livestock is added to the tank.

Live Rock
A protein skimmer (sometimes referred to as a foam fractionator) will remove organic pollutants from your tank. Protein skimmers create tons of tiny micro bubbles inside of their reaction chambers that dissolved organics are attracted to. Due to their hydrophobic properties (the need to get away from the water), the combined bubble and dissolved organics will rise up a tube and foam over into a collection cup. The end result is a very smelly, tea to coffee colored liquid called skimmate.

Many people have successfully run their reef tanks with only live rock and a protein skimmer, but other types of filters can be incorporated to perform an even better job. For example, a canister filter or fluidized bed filter can be used to help with chemical filtration (i.e. the use of carbon or phosphate media for example). I’ve tallied up some of the advantages/disadvantages of the most popular types of filtration for reef aquariums and recorded my findings below:

* Eheim Canister FilterCanister Filters & Hang on Back (HOB) Filters
PRO: They are excellent for adding carbon or other filter media to the tank and can even be good mechanical filters to help trap larger particles.
CON: If they are not cleaned often (every 2-4 weeks) they can lead to the build up (or source) of nitrates and phosphates in the tank due to food or other organics being trapped inside. Water will sometimes flow around the filter media instead of through it (in other words, water will take the path of least resistance).

* Fluidized Bed Filters
PRO: One of the best choices for using filter media, such as carbon or phosphate, in an aquarium. Due to their upflow principle, they will give the best contact between the tank’s water and the filter media of choice.
CON: It is generally not recommended to use more than one type of media inside of a fluidized bed filter, so multiple units may be required for using different filter media at the same time in a tank.

* UV Sterilizers
PRO: They can be very useful for controlling free-floating algae and algae blooms. Properly setup, they can help reduce free-floating parasites.
CON: UV sterilizers do not discriminate against good or bad organisms that flow through them, so they can kill off some of the good microorganisms in your tank.

* Ozone
PRO: When used properly, many aquarium hobbyists find their aquarium water is so clear, it almost looks as if there is no water in the tank.
CON: Ozone can be harmful if not setup properly. They are generally used with a protein skimmer and the air leaving the skimmer MUST be filtered by carbon to prevent any ozone from entering the air.

* CPR RefugiumRefugiums
PRO: Generally very good at nutrient export (mainly phosphate and nitrates, which are utilized by the algae growing in the refugium), refugiums provide a safe haven for microorganisms such as amphipods and copepods that can help feed fish and corals. They can also help stabilize the pH in an aquarium by utilizing the CO2 produced in the main tank when the lights are off.
CON: While small ones are available, in general they can take up quite a bit of space. Similar to the display tank, they will require regular maintenance to keep them running properly (such as pruning algae on at least a monthly basis).

* Wet/Dry Filters
PRO: Very good at breaking down toxic ammonia into the less toxic nitrate. They provide an aerobic environment for bacteria to work in (to break down waste), so they don’t deplete oxygen from the main tank.
CON: They are almost too efficient for a reef tank and may cause nitrate levels to build up too fast. The live rock in the tank should be plenty of biological filtration.

* Deep Sand Bed (DSB) or Plenum
PRO: When setup properly and given time, they will help create a denitrifying area in the sand bed (or void area) that reduces nitrate levels within the aquarium.
CON: For some people, a 4-6” deep sand bed or remote area can take up too much space in the tank. There are mixed opinions on the long-term efficiency of these methods; some feel they “trap” nitrates and eventually release them into the tank.

* Korallin BiodenitratorNitrate Filter (Denitrator)
PRO: Very efficient at reducing nitrates within the aquarium.
CON: Can be difficult to set up; fairly expensive and generally only suitable for larger tanks.

So what about hobbyists that don’t want to keep a reef tank with live corals and other invertebrates, but do want a saltwater tank with beautiful and colorful saltwater fish?

The truth is filtration for a fish-only (FO) tank doesn’t have to differ all that much from filtration on a reef tank in regards to setup. Eric Borneman wrote an article, Fish Only vs. Reef Only – What’s the Difference? that breaks down some of the major differences. To quote Eric, “I would recommend that using natural reef methods for all marine aquaria be the preferred method for both the success of the marine life, as well as the success of the aquarist.” I couldn’t agree more with his statement.

Of course, if you can’t or don’t want to use live rock in your tank, what choices do you have? Going back to the main topic of this article (filters), you will need a filter system that provides your tank with the best possible biological, mechanical and chemical filtration possible. Many feel a wet/dry filter system is your best choice, as they are very efficient at breaking down the waste fish produce. All of the filtration choices mentioned earlier for reef tanks can be used on a FO system and the same pros and cons will apply.


Filter media includes products like carbon, phosphate removers and ion exchange resins. These products help reduce and remove organics that cause problems like smelly water, yellow tinting to the water and problematic algae caused by phosphate and/or nitrate problems. They work by absorbing or adsorbing different organics/chemical from the water, helping to maintain high water quality within the tank.

* Red Sea MAX Activated CarbonCarbon: Carbon is probably the most widely used filter media sold today. There are two main reasons carbon is used; to help keep water clear from yellowing and to help with odors from the tank. As water passes by the carbon, it will remove pollutants that cause these two issues within an aquarium. This can be accomplished by placing carbon in a filter media bag and setting it inside a canister filter or by using it loosely inside of a fluidized bed filter.

* Phosphate Removers: The second most popular type of filter media helps rid aquariums of phosphates. High phosphate levels can actually inhibit corals and other calcium based organisms from being able to properly utilize calcium and magnesium. High phosphate levels can also lead to excessive algae growth. The two most popular types of phosphate remover media are the iron (ferric oxide) based media (Phosban, RowaPhos or Pura Phoslock for example) and the alumina based media (Phosphate Sponge or Phosguard).

Both have their advantages and disadvantages but, generally speaking, work fairly effectively. For reef tanks, most prefer iron-based media over alumina-based media since iron-based media can filter the tank for a longer period of time. Most alumina-based media needs to be removed within 24-48 hours after use. Another advantage that many overlook or simply don’t realize is that most phosphate removers will also remove silica from the tank’s water (once the phosphates have been removed). Silicates can sometimes cause outbreaks of brown algae on the aquarium glass, sand bed and/or on the rocks in the tank.

* Kent Marine Nitrate SpongeNitrate Media: Like phosphate, high nitrate levels can lead to problematic algae growth within the aquarium. Unlike fish, most invertebrates cannot tolerate high levels of nitrate. Many of the nitrate media products on the market are extremely porous and allow for anaerobic bacterial denitrification deep within the pores of the media (Nitrate Sponge and De*Nitrate are examples). Others, like Purigen or HyperSorb, are synthetic adsorbents that help remove nitrate (along with other organics).

* Mixed Resin Media: There are a few companies out there who make filter media that combines carbon with ion exchange resins, such as Boyd’s Chemi Pure and API’s Bio-Chem Zorb. These types of mixed resins come already in a bag and give the user a product that not only has the benefits of carbon, but also can help ionic balances (more stable pH).

With the proper filtration system, you will find your aquarium inhabitants will not only survive, but thrive within their glass (or acrylic) walls. But please don’t make the mistake of thinking that just because you have an oversized filter system or you use extra filter media on your tank that you can overstock, overfeed or neglect your normal maintenance. Every tank still needs some hands-on time to keep it running properly.

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