The Science of Protein Skimmers by Scott Brang


8 May 2007
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Point Waterfront Durban
Hey guys, came across this article and found it to be very interesting. Hopefully many of us especially our newbies might benefit from it.

Foam fractionation—better known as protein skimming in the aquarium industry—has been around for many years. Protein skimmers are one of the main pieces of equipment that have brought about long-term success for marine aquarists. That’s not to say protein skimmers are essential; many reef aquariums operate just fine without one.

The primary purpose of a protein skimmer is to remove organic compounds from an aquarium before they breakdown into phosphates and nitrates. They also have a beneficial side effect: aerating the aquarium. Excessive phosphates and nitrates diminish water quality, cause algae growth and contribute to health problems in both fish and coral. Skimming helps maintain a healthy aquarium environment by halting the phosphorus and nitrogen cycle, plus it removes toxins released by corals and other organisms. Water clarity is improved, too, since the compounds that cause yellow water are removed.

Before we get into which protein skimmer is right for you, let’s first look at the science behind foam fractionators.

A typical protein skimmer consists of a water-filled cylinder that is injected with bubbles. The bubbles “grab” waste and carry it upward into a collection cup. You then simply dispose of what is in the collection cup to remove the waste from your aquarium system.

Not too complicated, right? Not at first anyway. Let’s take a deeper look at the mechanism that the bubbles use to grab organic aquarium waste.

Most waste products in a reef tank are amphipathic or amphiphilic. If you don’t speak geek, that means one part of the molecule is hydrophilic (likes water) and another part is hydrophobic (dislikes water). This characteristic drives the molecule to seek a water/air boundary. This affects hydrophobic molecules, like oil, as well.

A good example of this is the “oil slick” that sometimes forms at the water’s surface in an aquarium.

Protein skimming takes advantage of this air/water interface to extract organics. Unfortunately, the surface area in an aquarium is small compared to the tank’s volume. To increase surface area and efficiency, protein skimmers inject tiny bubbles into the reactor chamber. Smaller bubbles work better (see included table, “The Science of Bubbles”), although if the bubble is too small it will not ascend into the collection cup.

Organics stick to bubbles due to surface tension. Unable to move from the bubble, the molecule rises in the chamber toward the collection cup. As bubbles climb inside the reactor chamber, they combine into foam and most of the water is drained out.

Since there are many different protein skimmer designs to choose from, they are generally classified by the way they introduce air to water.

[SIZE=+1]Air Stone[/SIZE]

The first protein skimmers used air stones to inject air. This method is still used today, albeit in smaller systems. They are inexpensive, only need an air pump to operate and have a simple, compact design. The design does have its downsides: the “stone” in most cases is actually wood and will need to be replaced every couple of weeks to maintain bubble size and density. Air stones are also not efficient enough for larger aquarium systems.


This method of air injection uses a (internal or external) pump to move water through a venturi which pulls air into the protein skimmer. This style of skimming produces a greater volume of air into the skimmer than air stones.

[SIZE=+1]Spray Injection[/SIZE]

This method of air injection is patented by AquaC. AquaC use a special nozzle to direct a spray of water into the protein skimmer body. This efficiently creates a large amount of bubbles in a small space.


Needle-wheels are currently the most popular way to introduce air into a protein skimmer. This method replaces the impeller in the input pump with one designed to shred air bubbles. A venturi is often used to bring air to the pump.

The popularity of needle-wheels has increased dramatically in the last couple of years. Many manufacturers now utilize this technology in their own designs. Deltec uses needle wheels in a recirculating pump in their AP series. This increases the contact time between air and water, allowing for more organics to be removed. Another company using the needle wheel is Warner Marine with their cone skimmer. Warner Marine combines a bubble plate and a cone-shaped body to reduce water turbulence and concentrate organics toward the collection cup.

[SIZE=+1]Location, Location, Location[/SIZE]

Design plays a big role in which type of protein skimmer will work for your system. There are three basic types: in sump, external and hang-on-back (HOB) or hang-on-tank (HOT). As the name indicates, an in-sump protein skimmer needs to sit inside a sump to function properly. An external protein skimmer can be plumbed outside of the sump, leaving more room in the sump for other equipment. A HOB protein skimmer hangs on the edge of an aquarium and is great for small tanks that do not have a sump.

[SIZE=+1]Which Type of Protein Skimmer is the Best?[/SIZE]

There are many things to consider when choosing a protein skimmer for your aquarium system. Every skimmer comes with a rating, usually in gallons or liters of total system volume. These ratings are just a general rule of thumb. If you have a 100-gallon aquarium with a large number of fish, you would be better served by a skimmer rated for a 150-gallon tank. It’s always better to go bigger when purchasing a protein skimmer. Look at your protein skimmer purchase as an investment. The cost of upgrading later on will certainly be more than buying a higher-rated model from the start. Plus, that way you can add more livestock down the road without worry. Obviously price will be a huge determinant when evaluating which protein skimmer to purchase. Protein skimmers range from extremely affordable to extremely expensive. Again, look at your protein skimmer as an investment. Often the higher-end models will save you time, money and headaches later on.

[SIZE=+1]Things to Remember[/SIZE]

The first question most new protein skimmer owners ask is “why isn’t this working?” A new skimmer will take several days to a week to break in. There are sometimes oils and residues leftover from manufacturing that also inhibit the skimming process. Also clean your skimmer often, every two to three days. A clean skimmer performs better. When cleaning, use a soft cotton cloth to avoid scratching the plastic or acrylic. Scratches can also reduce performance.

[SIZE=+1]Final question: Wet vs. Dry Skimming[/SIZE]

Is it better to collect a watery, diluted waste or darker, pasty foam? This debate is like the Coke vs. Pepsi of the aquarium world.

Wet foam contains slightly more waste products than dry foam, but is diluted with tank water. On the other hand, dry foam looks really impressive and you can brag to your reef friends about how awesome you are. Depending on how often you clean and service your aquarium system, one might be better than the other. Since the wet method contains more water, the collection cup may need to be emptied more frequently. One thing to consider with wet skimming: as more aquarium water is pulled out, the salinity of your tank may need to be adjusted occasionally as you top-off the water lost to skimming with freshwater.

If the foam you are collecting is less concentrated than you prefer (too wet), lower the water level inside the skimmer in small increments. This will give the foam more time to stabilize before it spills into the collection cup. If adjusting the water level in the skimmer doesn’t work, try closing off the air valve in small increments.

If the foam you are collecting is more concentrated than you prefer (too dry), verify that the pump air intakes are clean and unclogged. You can try to raise and lower the water level a small amount in either direction to see how this impacts the performance.
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nice one Mek !!
hey man thx nice info there :thumbup: very nice reading ,now......... if only i can find my glasses maybe then i can find my false teeth :razz:
awesome meks. great find. thanks
Hey Mek,
thank. i`ve been looking for answers the whole day about the F#@*n skimmer and was going on clueless, nearly threw the towel in.
that helped a lot!
Awesome read Mek, don't know how i missed this one...
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