VIDEO: A Beginner’s Guide to Protein Skimming

19 Jan, 2017


A protein skimmer is a device designed to clean the water in a reef aquarium by removing dissolved organic compounds.

Put even more simply, it is a controlled overflow of dirty water. Imagine a chamber that vigorously mixes air and water to create a dense foam. The cleaning action is because of the tiny bubbles in that foam. The surface tension of the tiny bubbles attracts dissolved organic compounds. As the bubbles slowly rise, a thick foam collects at the top of the skimmer and bubbles over the edge into a collection cup. By removing this foam, the water is cleaned because the dissolved organics are being eliminated before they have an opportunity to pollute the tank. In my opinion, protein skimmers are one of the most important devices for a reef aquarium.

Are Protein Skimmers Absolutely Necessary?

Can a hobbyist set up a tank without a protein skimmer? Sure. It is possible to do a lot of things in this hobby and still be successful. Is it recommended to omit a protein skimmer? No. A skimmer is one of those devices that just makes the hobby easier. It is one of those things that has such overwhelming benefits that removing it is just not worth the trade-off.

Types of Protein Skimmers

There are many types of skimmers, and they are grouped together by the method they use to create bubbles. These days, most of the popular designs use a needle wheel impeller that chops up bubbles. An older design uses a venturi to mix air and water. An even older design uses airstones and an air pump to create bubbles. All of these designs work, and it is a matter of personal preference and the constraints of the system that determine which type will work best.

If you really want to get technical, you can take a look at a book called Aquatic Systems Engineering, by Pedro Ramon Escobal. There are equations in there that look at flow rates and contact time to help determine skimmer efficiency, but to simplify things a bit for this video, bigger is going to work better than smaller, and more contact time is going to work better than less. Practically speaking, however, most installations do not allow for a massive skimmer. I would venture to guess that most skimmers in the hobby live in a sump inside the aquarium stand, so they are not often taller than 24”. This is part of the reason that a lot of skimmers are now a needle wheel design, and the body of the skimmer is shorter and fatter. Needle wheel skimmers, by design, take up a relatively small footprint and can squeeze a great deal of skimming power into a small body.

Buying Guide for Protein Skimmers

First, it is important for the protein skimmer to have a nice pump. A protein skimmer is an incredibly simple device, and if there was anything that could go wrong and break, 9 times out of 10 it’s the pump. It’s for this reason I am kind of old-school when it comes to skimmers because I like venturi skimmers powered by a Japanese-made Iwaki pump. Iwaki external pumps are the exact opposite of an energy efficient pump, but they are the most reliable pumps I have ever seen. I have never even heard of one failing, and some have been in operation for over 20 years. Unfortunately, I have not seen a comparable quality pump in needle wheel designs. There are plenty of expensive pumps, but none are as reliable as an Iwaki.

Second, I look at the valve that controls the water level in the skimmer. Earlier, I described skimmers as a controlled overflow of dirty water out of your aquarium. Well, the control part of that is very important. If the water level is not high enough, the skimmer is not really removing anything. If the water level is too high, the skimmer is removing the dirty water, but also a larger volume of water than necessary. Worst case scenario is it removes too much water and your return pump runs dry.

So, I want to see a nice quality gate valve to control flow of water leaving the skimmer. When you close down the valve, the water level rises. When you open it up, the water level falls. A higher quality gate valve will allow you to do this with great precision. Back when people built their own skimmers, some made the critical mistake of using a ball valve to control skimmer output rather than a gate valve. A ball valve is supposed to be for on/off applications, and a half turn of the valve would go from completely open to completely closed. It was nearly impossible to properly tune a skimmer. A gate valve, on the other hand, takes about 20 full turns to completely open or close.

Third, speaking of water exiting the skimmer, I like to see designs where the water exits above the water line where the skimmer sits. In other words, avoid designs where the output of the skimmer is submerged. The reason for this is that the water level might fluctuate depending on the system. and you want it to be consistent. Assuming for a moment that your skimmer sits in a tank that has a changing water level, the higher the water level, the more back pressure is put on that skimmer output. In essence, that is like closing down the valve raising the water level in the skimmer. This can cause the skimmer to over-skim. Once some water evaporates or enough water is over-skimmed out, the water level decreases and now there is less back pressure on that skimmer output. That’s not a great thing either, because now the skimmer may be under-skimming. By having the skimmer output above the water line, you avoid any chance of fluctuation.

An alternative is to place the skimmer in a section of the system that has a controlled water level, such as an overflow chamber of a sump. That would keep the water level constant; however, it is still possible for there to be fluctuations in the skimmer’s tuning here. The salinity of the water going up and down from evaporation or water changes affects the back pressure on the skimmer, and that can throw off its tuning.

Lastly, I want a skimmer that uses the fewest pumps possible. There are some skimmers out there that use a whole bunch of pumps to generate foam, sometimes as many as four. My problem with these designs isn’t so much that four pumps is overkill, but remember what we discussed earlier? The most likely thing to break in a skimmer is a pump. Now that problem is multiplied by four. One might think that if one fails, at least you have three others as backup!

The problem is, if one pump fails, the skimmer still stops functioning properly because it was tuned to the flow rate of four pumps. Now there are only three pumps, so that protein skimmer doesn’t actually skim until it’s re-tuned.

Troubleshooting Protein Skimmers

Let’s take a look at some common problems that you may experience with a skimmer.

Problem #1: Oils and other chemicals

First off, skimmers are sensitive to oils and other chemicals introduced into the reef system. The bubbles, after all, work by surface tension and hydrophilic interactions. Oils from your hands or from food can shut down skimmer’s production for hours. Even a water change can throw off a skimmer temporarily. If you encounter this, there is not a lot that can be done about it; you just have to wait it out.

Problem #2: A blockage in the pump

A blockage can happen in any skimmer design. A piece of debris that gets stuck in a venturi or in a needle wheel can throw off a skimmer’s performance, so it’s important to regularly take your skimmer apart and clean it to make sure there are no obstructions.

Problem #3: A blockage of the air intake

Speaking of obstructions, it is a good idea to check the air line to see if it is blocked. A skimmer’s job is to mix air and water, but if the air intake is blocked somehow, that air-water mix gets thrown off where you are getting more water than air. The very nature of the air line makes it prone to forming solid deposits that eventually block the intake.

It’s tempting to just fiddle with the gate valve to adjust it to calibrate the skimmer, but what can sometimes happen is that the obstruction works itself free and suddenly there is a huge rush of air and your skimmer looks like a foam explosion the next day. So, again, keep your skimmer clean and well-serviced.


In summary, a protein skimmer is one of the most helpful devices in the reef-keeping hobby for maintaining clean water. Hopefully this article was helpful in shedding some light on the subject of skimmers and what to look for the next time you purchase one. Until next time, happy reefing.

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About the author

Than Thein
Than Thein

Than is the owner of Tidal Gardens and Advanced Reef Aquarium. Than's background is a mix of biology, computer science, business, and law. However, the reef aquarium hobby eventually led him away from a suit and tie corner-office job to pursuing his passion growing coral and shooting underwater videos.


  1. January 23, 2017

    Great video! Was wondering what that blue Xenia looking coral was at the end of the video with the page heading “oils and chemicals”?

  2. January 23, 2017

    I believe that is a Blueberry Gorgonian

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