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Q10918 - INFO: The Science of Protein Skimmers by Scott Brang, a Marine Depot Staff Member
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.

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

Air Stone

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.

Venturi Diagram
Spray Injection

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.

Needle-Wheel Impeller
Location, Location, Location

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.

Which Type of Protein Skimmer is the Best?

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.

Things to Remember

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.

Final question: Wet vs. Dry Skimming

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. And, of course, if you have any additional questions about protein skimmers, contact us! We’re happy to help.
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Approved Comments...
very nice Approved: 7/7/2014
At the beginning of this article, the author said that protein skimmers arent essential, that you can maintain a reef aquarium without one. He should explain more why they are not absolutely essential, since the whole article is telling us how great they are! Also, what exactly are dissolved organics??? Where do they come from? Why are they in the tank? If the author can answer these questions satisfactorily, then I would rate this article a 10! Approved: 8/28/2011
Very easy to understand, I had just installed a protein skimmer and couldnt figure out how it worked. This article cleared up my conceptions. Approved: 1/22/2010
it covers just about everything one has to learn about ps Approved: 1/22/2010
simple and straight forward - not too complicated. Approved: 6/12/2009
Tops article. One phrase I didnt hear: beckett method? Approved: 6/11/2009
Because I have a relatively large skimmer and only two fish (plus some crabs and live rock with critters)in an 85 gallon tank. I rarely change the water and have had few problems over the years. After reading your article it appears that getting a good skimmer (Red Sea Turbo) may have been one of the best things I have done. Also, the wet vs dry discussion was something I have always wondered about. Finally, I never knew how the bubbles attracted the wastes that ended in the collection cup. Approved: 6/10/2009
good info on the different ways to skim in saltwater tank. Approved: 6/9/2009
Just overall great information. Approved: 6/8/2009
This is a good read. Approved: 6/8/2009
Basic but concise info - how about an advanced article? Approved: 6/8/2009
good info Approved: 6/7/2009
Very informative and to the point for the need for a protien skimmer. I believe that any body who is going to keep these animals should buy the biggest one that will fit in there system and thier pocket can afford. saves many headaches later. Approved: 6/7/2009
You have collected the info on how skimmers work and the varieties of methods of creating the bubbles in one concise article that is easily understood by the layman. Well done. Approved: 6/7/2009
I knew basically how skimmers worked but the author was very good at explaining it in laymans terms. I also learned something new about my system which I appreciate. When you are not someone who is very scientific, it helps to hear information over and over again and written in such easy-to-read format. Reefer for a little over a year. Approved: 6/7/2009
I have been struggling lately with high nitrates. Been cutting back on the amount of food for the fish, less uneaten food & less poop. Very little difference. I forgot about the protein skimmer. Will examine the issue closer to see if that can help. Approved: 6/6/2009
I was just advised to buy a protein skimmer and simply told that it would help the quality of my water but this information goes more indepth and the real importance and benefit of having and using a protein skimmer. Approved: 6/6/2009
Great description of the protien skimmer in laymans terms except for the bubble chart Approved: 6/6/2009
pretty basis Approved: 6/6/2009
Very informative on how skimmers work. I recently upgraded my skimmer after my old one died and although I am happy with my choice, I wish that I had this article to read at the time of my search. Approved: 6/6/2009
Good information,easy to read. Approved: 6/6/2009
Excellent overview of protein skimming and the current methods used by the various manufacturers. I did not feel there was any favoritism to any one manufacturer an error commonly made by retailers to push what they carry. It took me years to learn what is in this article. I have gone the gambit from the air stone skimmer (all there was 20 years ago) to the needle wheel venturi skimmer, which BTW really are fabulous! Unfortunately, my experience with skimmers is they require frequent "fine tuning" to work their best and the need to keep them clean can not be over emphasized. Approved: 6/5/2009
I didnt know about the needle wheel. I will look into it. Approved: 6/5/2009
Article Details
Created on 6/4/2009.
Last Modified on 6/5/2009.
Last Modified by Dot Yuson.
Article has been viewed 13878 times.
Rated 8 out of 10 based on 122 votes.
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