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Water treatment and filtration in the marine aquarium.

Heating with heater(s) and cooling using a chiller and/or fans takes place in the sump area.

You also create your own water treatment plant — often times called the “Berlin Method”.

(1) Live Rock provides a substrate for bacteria that “eat” waste materials.
(2) Deep Sand Bed (DSB) works in much the same way as live rock. Be careful here. Many reef keepers are moving away from a DSB to something shallow for looks or even bare bottom.  Is a DSB a ticking time bomb?
(3) Partial Water Change removes and dilutes waste materials to a certain extent, and adds back key minerals that are depleted by the animals.  Change 10% of display tank volume monthly as a rule-of-thumb.  Consider smaller more frequent changes.
(4) Protein Skimmer can be used to further remove harmful organic compounds.  Do skimmers remove the good with the bad?
(5) Refugium in the sump area, and/or algae scrubbing (ATS) uses marine algae to “eat” waste compounds and chemicals (nitrates and phosphates), to out-compete (hopefully) algae in the display tank (DT), and add oxygen to the water through photosynthesis. Like a mangrove swamp in nature.

3-5 times your display volume per hour through your sump should be sufficient for filtration purposes.  See overflows.


Biological Filtration

Bacteria and algae. Live rock, live sand bed in the display tank AND sometimes in the sump. Algae/seaweed usually in the sump/refugium but also in the display tank.

Mechanical and Chemical Treatment and Filtration
Filter sock, protein skimmer, phosphate sponge, carbon, ozone, UV.

Protein skimmer


Department of Chemistry, The Pennsylvania State University: “In contrast, perhaps one of the more interesting observations to emerge from these studies is the fact that all four skimmers tested removed only 20 – 30% of the total organics present in authentic reef tank water.”


Tom Murphy: “There has been a great debate for years on whether one can/should run activated carbon in a reef tank. The anti-carbon argument takes the position that carbon removes beneficial material that coral and other inverts consume. I have never heard a convincing explanation of what this supposed food consists of or what it does for these organisms. Carbon is used to remove dissolved organic compounds from the water. The effect of DOCs could be to merely cause the water to take on a yellowish appearance they can consist of complex organic toxins produced by the creatures in the tank. Dissolved substances are not directly absorbed by higher animals and are mainly consumed by bacteria and algae. Coral, anemones and similar critters don?t directly consume dissolved organic materials. The zooxanthellae in corals don?t benefit much from dissolved organics as they get their nutrients directly from the coral and the uptake is extremely fast. It is highly unlikely that running carbon 24/7 removes any material that is essential to the livestock in a tank. Carbon improves water quality and reduces bioload on the tank, so I would say to go ahead and use it.”

How To use Activated Carbon, from Joe Jaworski’s Weblog

? For ongoing maintenance, I recommend 1 cup per 60 gallons of water. This is a bit higher than most suggestions, but using more carbon works faster and lasts longer. Double this amount for tanks with obvious signs of high organics or first time carbon use in poorly maintained tanks.

? Filter the water mechanically before it reaches the carbon. Particles greater than 100 microns in size will take a toll on the life of the carbon.

? Despite popular belief, carbon does not need to be placed in a canister filter or a compartment where all tank water passes through it. Dropping a mesh bag full of carbon into the sump works fine. This is because carbon works by electrically attracting particles- it is not an inert mechanical filter. Studies have shown that bags of carbon in a sump with moderate flow removes substantial quantities of organic pollutants, medications, and heavy metals. Actual performance depends on the flowability of the bag material. It is most effective if you use a media bag with the largest possible hole sizes but small enough where the carbon cannot escape.

? For the average marine fish aquarium, carbon will last 6 weeks. Reef tanks produce more organics than fish-only tanks, so 4-6 weeks is a workable limit. If the water is not mechanically filtered or the aquarium shows signs of nuisance algae, you will need to adjust the useful life or increase the amount of carbon.

? There is no effective way for the aquarist to either recharge carbon or measure its rate of exhaustion. I have experimented with the Salifert Organics Test Kit to measure carbon life, but I was unsuccessful because the range of the test kit would not allow me to measure steady declines over time. Don’t re-use carbon or try to clean it. Recharging carbon requires a specialized high temperature/low oxygen oven that would be prohibitively expensive at this small scale. The best solution is to replace the carbon at 4 to 6 week intervals.





Aq Pharm Black Magic®


Kent Reef Carbon®


Boyd Chemi-Pure®


Hagen® Fluval® Carbon


Hydor Prime®


Lifegard® Pelletized


Marineland Black Diamond®




Seachem Matrix®


T.L.F. Hydrocarbon®


Warner® Granular



Activated Carbon Myths and Misconceptions

? Carbon removes trace elements- Carbon has a greater affinity for organics than trace metals, but it will remove some trace elements. On the other hand, both protein skimming and natural consumption of trace elements by tank specimens will remove significantly more trace elements than carbon. Aquarists concerned about depleted trace elements should be using a trace mineral additive- whether or not carbon is used. Two excellent products for this are the Sera Strontium Complex and the Seachem Reef Trace products.

? Carbon will leach organics back into the water False. Once all the carbon pores are saturated, bacteria slime and detritus will accumulate on the carbon grains, turning it into a weak biological filter with the organics locked in the deeper layers.

? Carbon should be used only a few days a month False. This myth was likely started by activated carbon’s ability to remove yellow tinting and odor from the aquarium within the first 48 hours of application (or perhaps manufacturers who want to sell you more carbon). The higher concentrations of organics are colorless and odorless and require more contact time for removal. Another complication of part-time carbon use is storage and reuse. Once the carbon is removed from the aquarium it will continue removing contaminants from the air. Placing the damp carbon in a sealed plastic bag doesn’t work either, as the damp carbon becomes exhausted servicing die off in the stagnant aquarium water stuck to the grains.

? Spilled carbon causes harm to the aquarium – False. Carbon granules that are accidentally spilled into the aquarium will quickly become saturated with bacteria slime, having the same biological effects as a grain of gravel. It may look ugly, but it is totally harmless.

As we have seen, the use of Activated Carbon is an important part of maintaining a healthy marine or reef aquarium. It is the only filtering media that can remove substantial amounts of metabolic wastes (organics), which accumulate over time and can prevent secondary water quality and health problems in specimens. Because of the phosphate issue in lower quality products, it is better to spend a little more on a quality carbon than use any carbon at all.

UV Sterilizers

Tom Murphy: “Not a myth, as they do work, but somewhat questionable for use in a home tank, is the UV sterilizer. They do work as advertised and can kill bacteria, algae and protozoa; it is a ciliated protozoan that causes ich. The main question is, do they prevent disease in the tank? In the display tank, disease prevention is highly unlikely unless the unit is extremely large. The filtration rates for common units are usually not high enough to kill a significant number of organisms to prevent infection. They also kill off protozoa that are food for corals and copepods. UV sterilizers can be useful under specific circumstances. In the case of multiple tanks connected to a common sump, a UV sterilizer placed in the return line to the displays can provide a barrier against disease moving from one tank to another. In this case, all the water is exposed to the UV light and the discharge water will be almost pathogen free. Another use is in the quarantine or hospital tank. These tanks are generally small and the use of a UV can help remove many pathogens. This is especially true if dip methods are used to control the disease, a UV sterilizer can kill emerging parasites not killed by the dip. For a large display tank there are better uses for your money. A canister filter with a micron cartridge can filter far more water and remove more pathogens than a UV. They also cost less than many UV sterilizers. I don’t advocate the full time use of a canister unless the filter element is cleaned at least weekly, but in an infected tank it will usually do a better job at removing disease causing organisms.”

Biopellets and carbon dosing