Saltwater Aquarium Filtration


Filtration is the most critical element to a healthy saltwater aquarium.


Essentially it is the process of removing dissolved and undissolved organic waste from the water, which if left to breakdown will cause the level of toxic compounds to build up to concentrations that can easily kill marine life.


Organic waste comes from:

⪼ Fish excrement
⪼ Food
⪼ Scales
⪼ Algae
⪼ Detritus
⪼ Dead organisms


So good filtration equals good water quality and a stable, healthy aquarium environment. Do not take short cuts or cheap options here.


In the ocean the sheer volume of water instantly dilutes these waste products, not only that there are hundreds of different marine organisms that feed off one form or another; nothing is wasted down to the last molecule.


In your aquarium there is a very different story because of the small volume of water in a closed system and the lack of diverse organisms to completely break it all down: this means we need to employ filtration devices to help do natures job for us.


The area of filtration can be a very complicated and confusing one to the uninitiated, there are quite a few different types of filtration and let me tell you not all of them are necessary in your saltwater aquarium. And for every different type of filtration there are a huge number of options….


Different types of filtration


Lets start by looking at the different types of filtration:


Mechanical filtration

Removes undissolved organic matter such as debris and uneaten food particles from the water using mechanical filters that sieve the water.


This aids biological filtration by removing a lot of the waste at the source before it is broken down. Suspended solids affect your water clarity and if you can get to them before they dissolve and breakdown into ammonia all the better.


As well as biological filtration and physical filtration (protein skimming) all marine systems should have some form of mechanical filtration.


Luckily these days a lot of biological filters have a mechanical component built in often as a prefilter. Be wary of mechanical filtration in a reef aquarium as this can remove the corals food (plankton, detritus), so turning it off while feeding is a good idea.


Also in an aquarium with live rock mechanical filtration is less necessary as the life contained in the live rock processes suspended waste effectively too.


Mechanical filtration media can be any number of different unreactive materials such as sponge or wool and will need to be cleaned out or replaced every few weeks or so as this is dirty waters first obstacle in the filtration process.


Physical filtration

Protein skimming is by far the most vital component to effective water cleaning. This method of filtration is so effective at clearing and oxygenating the water it is considered an absolute MUST for any marine aquarium and is secondary in importance only to biological filtration.


It serves to get rid of dissolved organic waste before it is mineralized into ammonia, thus greatly reducing the load on biological filters which reduces the strain on the system and helps keep nitrates down.


Protein skimming uses fine bubbles to attract protein molecules usually from the aquarium water surface in a chamber to attract and remove dissolved organic waste from the water column via foam as a concentrated, smelly brown liquid which is channelled into some kind of collection cup to be discarded.


Most people are amazed how much gunk comes out of their aquarium water in this fashion. You cannot over skim a marine aquarium in my experience.


The “natural” or Berlin system uses only a large volume, high output protein skimmer, mechanical filter and live rock as the foundation of its filtration requirements. Often there is also a wet/dry filter (without the wet/dry chamber) with prefilter and sump containing the protein skimmer as well.


Chemical filtration

The main component of chemical filtration is activated carbon and this should be placed after mechanical and biological filtration has taken place so the chemical media is not fouled up.


This has most common application in reef aquariums where water quality is of higher importance.


Chemical filtration removes unwanted metabolites, coloring and chemicals from the water as a last stage treatment option.


Chemical filtration is not absolutely necessary if you are cautious about what goes into the water but does have its use in high water quality generation especially in reefs.


For most applications the activated carbon simply sits in a nylon bag in the filter housing through which the water is passed, the activated carbon/charcoal “scrubs” up phenols and heavy metal contaminants.


If you plan to use carbon, 200-250g per 100 litres is a good amount to begin with. Carbon will intermittently need to be changed after 3 to 6 months as its ability to absorb chemicals will markedly decrease after time.


Another important aspect of chemical filtration is phosphate removal as this compound can get into the water in a number of ways (overfeeding, detritus, phosphate containing additives) and will essentially over fertilise the water resulting in unwanted, out of control algae outbreaks.


Phosphate reactors with special media can effectively reduce phosphates, which is especially important in reef aquarium environments.


Biological filtration

By far the most crucial type of filtering to any saltwater aquarium, this is a service performed by marine bacteria feeding on dissolved nitrogenous waste and is part of the nitrogen cycle.


Waste is excreted from marine life in the form of protein, which is quickly mineralized into ammonia/ammonium (NH3 or NH4); ammonia also comes from the breakdown of food particles and decaying organisms.


This ammonia is highly toxic to marine life, but luckily nature has a solution for us in the form of a marine bacterium (Nitrosomonas) who use this substance as their energy source and aerobically convert it to nitrite (NO2).


Nitrite is less toxic but still nasty, yet another bacterium (Nitrobacter) then comes along and converts nitrite to the less harmful nitrate (NO3).


This process is known as nitrification and you will need test kits to keep tabs on these levels in your saltwater aquarium.


The final phase is denitrification where anaerobic bacteria in oxygen free environments convert the nitrate into harmless nitrogen gas bubbles. These anaerobic zones can be found in the interior of live rock and live sand; you can also purchase commercial denitrification filters that harbour these bacteria.


The challenge of denitrification in a marine aquarium is to keep up with the nitrate levels being generated as nitrification occurs at a much faster rate than denitrification so nitrate levels can slowly rise over time.


An effective biological filter will have plenty of surface area for the bacteria to grow (filter media includes balls, sponges, fibres, floss, beads and many others) and will be supplied a constant source of well-oxygenated water and obviously ammonia to use for food.


These beneficial bacteria will eventually colonize any surface and will grow as a “biofilm”. You must be careful to nurture this bacterial growth as damaging the bacteria can cause your aquarium to crash.


The best biological filters are natures ones: live rock and live sand.


These natural substrates are harvested from tropical waters and are jam packed with beneficial bacteria and tiny marine organisms that will literally come to life in your aquarium.


This not only gives your tank a natural look but gives marine fish a place to hide and is packed with not only beneficial micro organisms but interesting algae and entire tiny invertebrate eco-systems.


The rock harbors both aerobic and anaerobic zones which will see biological waste not only broken down to nitrate but converted to harmless nitrogen gas; the complete marine nitrogen cycle.


Live rock is weight by weight the most expensive item for saltwater aquariums but is well worth the investment.


Power filters

Excellent options for smaller and fish-only aquariums, they come in many forms such as inside, outside, “hang on back” and canister.


Power filters pump water from the aquarium, filter it in a box using a sponge type filter then pump clean water back.


They often come with mechanical filtration built in and have space for chemical filtration media. They are excellent multi-purpose filters and are easy to maintain, require the least amount of care, adapt quickly to increasing bioloads and they also aid water circulation.


Wet/Dry (trickle) filters (a.k.a. reef filters)

These are my top choice for medium to large or heavy bioload aquariums as they are easily the most capable filters at providing good water quality and provide a high level of oxygenation.


Therefore they are a definite best choice for reef set-ups and biologically filter the water seriously fast and can often provide biological, mechanical, physical and chemical filtration all in one package.


These filters are usually reservoirs beneath the aquarium and are mostly in 2 parts, the wet/dry chamber and a sump area which can contain a number of water treatment options such as live sand, protein skimmers, denitrification filters, phosphate removers, dosers.


The principle is to maximize the air-water interface by “trickling” the water over unsubmerged filter medium (dry area) which highly oxygenates it, the water is then directed to a wet area where it is additionally treated chemically and/or physically.


Often these filters mechanically filter (sometimes using a prefilter) the water as it is entering the system too.


The wet/dry (trickle) filter is very efficient and results in outstanding clean, oxygenated water being pumped back into the aquarium.


Fluidized bed filters

Relatively new technology that sees the biological filtration take place in a sleek tower unit separate to the aquarium where water is pumped up the chamber suspending the media (sand or similar) inside which is coated with beneficial bacteria providing excellent circulation and an unmatched surface area for efficient biological filtration. If these units are large enough they can contain an anaerobic zone for denitrification.


Fluidized bed filters are especially good for large and heavily stocked aquariums. They cope well with rapidly increasing bioloads and are very efficient and self-cleaning.


As you can see filtration plays a very important role in our marine aquariums removing undissolved and dissolved organic waste and is the key component in good water quality.


Good biological, mechanical, physical and sometimes chemical filtration will serve to create the pristine water environment marine life needs to truly thrive.