Fish, Tanks and Ponds

Fish, Tanks and Ponds
A comprehensive guide to fish

The Protein Skimmer

Protein Skimmer


Imagine taking a walk along the beach beside the ocean, you look down at the edge of the water and see the patches white foam. You stop and wonder, what causes that foam or if it has any real purpose being there?


The foam that you have seen is the basis of a wonderful filtration tool available and used mainly in the Marine hobby. The process is called foam fractionation and is more commonly referred to as a protein skimmer. The process of protein skimming is amazingly simple and a highly effective way of removing organic molecules from water. Protein has an interesting characteristic in that one end of the protein molecule is hydrophilic (attracted to water) and the other end of the molecule is hydrophobic (repelled by water). When protein molecules come in contact with air passing through the water, the end that is hydrophobic will stick to the air bubble and the part that is hydrophilic will remain in the water. Eventually the protein is brought to the surface and creates dense foam that can then be collected and removed from the water.

Protein skimming

The advantage of using a protein skimmer on an aquarium is that it removes organic compounds from the water before the filter bacteria breaks it down, creating less work for the bacteria, which translates into less nitrates in the water. The main disadvantage of this process is that protein is not the only thing that attaches to the air bubbles and eventually gets removed from the system, but essential trace elements also get removed.

Since the process of skimming the water is so simple to replicate and creates a lot of benefits to an aquarium, there are many different methods and models of commercially available protein skimmers for sale. So, how do you tell which are the best models and which model is best for your system?

When looking for a protein skimmer there are a couple main points that need to be considered. One of the most important operational considerations to look for in a skimmer is the size of the bubbles the skimmer uses. The finer the bubble the more surface area to size ratio the bubble has, meaning that more protein molecules will be able to stick to the bubble. The number of bubbles the skimmer produces is also important to consider. The more bubbles, the better for the same reason as why you need fine bubbles, more surface area!

Protein Skimmer
Air stone Driven Protein Skimmer

Another consideration is the rate of flow through the skimmer. This is a very tricky balance to figure out. The longer the bubbles can remain in the water column, the more efficient the skimmer is. If the water is flowing through the skimmer too fast, the protein doesn't have enough time to attach to the water, and too slow doesn't filter very much water. The flow rate also depends on the length and width of the chamber. Generally a narrow chamber will have a faster flow rate then a wide chamber and a short chamber will provide a shorter contact time then a longer one. A properly sized skimmer should turn over your tank volume about 3 to 5 times an hour while providing the most air/water contact time possible.

There are many different ways to inject air bubbles into the reaction chamber of the skimmer. I will only talk about the most common methods available.

Some of the first commercial protein skimmers used an air stone to inject the air bubbles into the skimmer. The best air stone to use is a block of lime wood as this produces very fine bubbles. The pressure of the air would lift the water from the bottom of the reactor and out the top like the way an under-gravel filter works. This model was then improved upon by adding a powerhead to pump water through the chamber, increasing the flow rate through the tank allowing more water to be skimmed. Even with a powerhead attached to the skimmer, it still has a fairly low rate of water flow. The advantages of this system is you can adjust the number of air bubbles by having a powerful air pump, but you have limited control over how much time the air stays in the water column and how fast the water flows through the system, even with a decent powerhead.

The airstone drive skimmers can be built as an in-tank and hang on back models for smaller tanks or systems with limited room and are good for tanks that can't have a lot of water flow, but they aren't as efficient as some of the other types of skimmers available. The airstone will also need to be replaced regularly as it will clog up with debris and protein fairly quickly.


The next generation of protein skimmer uses a Venturi style pump to inject air into the water column. A Venturi pump is basically a modified powerhead that sucks air in and mixes it with the water being pumped. This process mixes the air and the water very well and allows for more air/water contact time then the air stone driven type of skimmer. The major drawback is the Venturi pumps can be fairly noisy depending on size of the pump. Even though the original Venturi style pump was very good at mixing the air and water, there was still room for improvement. Eventually, a propeller was added after the air was sucked into the water column, which allowed the propeller to chop up the air bubbles into even smaller air bubbles. This created more surface area and a more efficient skimmer.

Venturi style skimmers can come in hang-on-back style models or stand alone units that sit on the floor and can be plumbed into the tank. This style of skimmer is able to handle fairly large size tanks, are efficient and can process large amounts of water. Depending on the model, they can be very easy or very difficult to setup. The main disadvantage to this style of skimmer is the potential for creating noise and the can be fairly bulky in size. The Venturi opening can clog fairly easily with a piece of sand or floating particle, so the pump needs to be properly monitored and cleaned on a regular basis.

Down-draft skimmer

One of the most advanced style of skimmer is called a down draft skimmer. The downdraft skimmer mimics the natural skimming process most effectively. With a downdraft skimmer, you have a tall chamber filled with hard objects such as bio-balls or live rock and the water is poured over top of these objects. As the water bounces off of the objects, it splashes around and mixes with the air in the chamber. The water then falls into a holding tank where the many fine air bubbles that was mixed into the water has time to rise, bringing the protein along with them. A baffle system is then used to ensure that no air bubbles can be pumped back into the main tank.

Downdraft skimmers are one of the easier models of skimmers to use, however they are very large units. Some can even be over 6 feet high. They are fantastic for very large tanks and can turn over incredible volumes of water. They require a lot of space when used on a home tank and are only available as stand alone units. They require a high powered pump to handle the amount of water passing through the skimmer at any given time.

There are a couple other ways for a skimmer to inject air into the system, some are more or less effective then other methods. Most of the other methods are patented processes and it's best to contact the manufacturer of the skimmer for more details on how they work.

Each type of skimmer has its advantages and disadvantages. They all work and each one has it's proper place and usage. For example: Having a downdraft skimmer that processes large volumes of water on a nano-tank would be pointless. The current in the tank would be so great nothing would be able to live in it. However an airstone driven skimmer would be idea for the nano-tank because they are relatively smaller then the other skimmers and it is a much slower turnover rate so it wont overpower the inhabitants of the nano-tank.

Now that you know the way skimmers work, you need to figure out some of the other limiting/deciding factors you need to look for in a skimmer model. Some questions that you should ask yourself when looking for the best skimmer

How much room do you have for a skimmer? Do you have room to have the skimmer sitting on the floor or in a sump or hanging on the back of your tank? If you have decide on a stand-alone unit, what other equipment will you need, such as bulkheads, plumbing, or pumps? How easy will it be to maintain the skimmer? Will you need to clean out the collection cup each day or does it come with a drain attached so you can leave it for longer periods of time? Will you need to buy replacement parts like airstones or pumps and how easy is it to find the replacement parts for the skimmer? What are the instructions like for setting up the skimmer are they easy to follow, or do you need a science degree to figure it out?

Purchasing a good protein skimmer for your tank will make maintaining your tank easier in the long run. It's better to spend a little more money buying the right one for your tank the first time then it would be to go out and have to buy another skimmer later. Remember there is no one best skimmer around and there are a lot of good models on the market for you to chose.