How Does A Protein Skimmer Work (Saltwater Filtration)

Daniel78, CC BY-SA 2.5, via Wikimedia Commons
Daniel78, CC BY-SA 2.5, via Wikimedia Commons

How Does A Protein Skimmer Work (Saltwater Filtration)


So you are thinking about investing in a protein skimmer but are not sure what exactly it is or what the differences between models are. There are a lot of good reasons why someone might want a protein skimmer but sometimes they are not all necessary for the success of your fish community. Protein skimming can certainly help with improving the water quality of your tank but protein skimming can be very ineffective if done improperly. It is important to take the time to learn more about how protein skimmers work so that you can effectively install one and make the most of your purchase.

Different Sized Protein Skimmers

30 Gallon Skimmer

For small tanks without a sump, hang-on skimmers are great.

65 Gallon Skimmer

Small tanks with a sump are better off using an in-sump skimmer.

100 Gallon Skimmer

Larger tanks need larger skimmers, but larger isn’t necessarily better.

150 Gallon Skimmer

Large skimmers are expensive and sometimes include adjustable pumps.

What are Protein Skimmers?

You have probably heard the name a few times from fellow hobbyist friends or on online forums but what exactly is a protein skimmer and why are they discussed so much? A protein skimmer is a device that uses air bubbles to remove waste and organic compounds from your saltwater tank’s system.

How does a protein skimmer work exactly?

Protein skimmers work by rushing air through the water to whip it up into a foam in the skimmer’s reaction chamber. It is the creation of these microscopic bubbles that remove the waste from the tank and carry it through the process. The waste actually collects on the microscopic bubbles and thus they can be transported effectively. When the microscopic bubble pops, the waste that it was carrying falls into the collection cup and thus it has effectively removed the waste from the aquarium water. How the bubbles can do this is that the bubbles e due to the properties of air and water. The air and water relationship created by the bubble surrounded by the water helps to charge the waste molecules in the water.

The charged waste molecules now want to stick to the bubbles as they float their way to the top of the column of water where they pop dropping off the waste the bubbles collected. As you might imagine, since the bubble is used to collect waste from the water, the size of the bubble can help in the collection process. The creation of the bubble size is crucial in the effectiveness of the protein skimming. It is the creation of this foam or air bubbles, that helps to collect the waste and bacteria from the aquarium. Most skimmers work to improve water quality as its reaction chamber overfills with foam, the foam drops down into an outer collection cup effectively removing the dirty organic wastewater from the main saltwater tank which is often called skimmate. The hobbyist only has to remove the collection cup from the skimmer, clean it, and replace it once a week. Protein skimmers can be a great way to help keep your saltwater aquarium clean without as much manual labor.

Are protein skimmers necessary?

No, protein skimmers can be a completely optional piece of saltwater aquarium equipment. Protein skimmers can make your life as a hobbyist much easier if properly utilized but sometimes you don’t even need it depending on the setup you plan to have for your aquarium. If you have it in your budget, a protein skimmer can be an invaluable time-saver, but you can just as easily get by with frequent and consistent water changes and following aquarium care best practices as outlined in other Reef Tank Resource articles like this one.

What is your planned setup?

You also want t to consider the type of setup you are hoping to have for your tank. If you hope to keep SPS or LPS corals in your saltwater aquarium, you might want to consider investing in a protein skimmer. Since these corals have high demands when it comes to the quality of their water. They will need more than just some basic filtration to keep their water pristine for healthy growth.

Does size matter? Bigger is not always better

Though in many cases, size might not matter, when it comes to protein skimmers, you want to be careful what size you are purchasing for your aquarium. Protein skimmers come in many different sizes and these sizes play a role in how effective they will be with your specific tank. Protein skimmers that are too small, or even too large, will not be as effective in cleaning your saltwater aquarium as if it was properly sized. When you go too large with a skimmer, there will not be enough organic compounds in the tank for the air bubbles to whip up enough foam that would collect in the reaction chamber. A small protein skimmer won’t be as effective as a properly sized one but it will work, unlike the oversized skimmer. If you are unsure and want to take the risk, you should definitely aim smaller than larger when it comes to skimmers.

So, what is the proper size for your tank? Protein skimmer manufacturers provide some guidance and tips for purchasing the correct size of skimmer but depending on your setup and experience these tips might not be completely accurate. To get a clearer understanding of where you might stand with your current set up, you need to take stock of a few things in your saltwater aquarium first, before you can begin looking at skimmers. What is the specific bio load that you are dealing with in your saltwater aquarium? The bioload is the total waste in the water column. The bioload comes from the waste of everything that is in your tank. There is no one definitive way to test for bioload in your saltwater aquarium. You can try to think of the bioload as representative of the food that you feed your fish. For instance, if you feed your fish a large variety of food every day, you might consider the bio load to be large. On the opposite side of the spectrum, if the total food you give to your fish is like a single cube of food it could be a small bioload.

What other types of filtration are represented in your aquarium’s setup? If you have other methods of filtration that act as a way of breaking down the total organic waste in your aquarium before it can reach the water column in your aquarium, the bioload will be much less to consider for the skimmer. Since the protein skimmer does not need to work as hard for as much of a bioload due to the other filtration systems, it might be that it is too large for that particular set up, even if you are dealing with a very large tank. However, if the protein skimmer is your saltwater aquarium’s main source of filtration then you might opt for a larger skimmer. If you have an elaborate filtration system, aim for a smaller model of the skimmer. It will still benefit your tank and you don’t risk the protein skimmer being too big for your aquarium.

Now consider when you installed your protein skimmer. If you installed the protein skimmer early, before the tank had all of its inhabitants, then the skimmer may be just fine in the future when the aquarium is full. Don’t install the skimmer and think that just because it isn’t working right this second that it won’t be good later. If you know that you have more to add then it might be prudent to wait a little bit rather than buy a new protein skimmer. However, if you bought a skimmer last as an upgrade then of course this guidance isn’t worth squat, and you might consider downsizing the skimmer. There are also protein skimmers that can have a wider range of settings which allow you to scale the skimmer to the appropriate bio load levels of the tank you are currently working with. There are also calculators to help you determine what your bio load might be. The problem with this is that many people question the accuracy of the calculators. Overall, it comes down to experience and sometimes trial and error to find the best protein skimmer that works for you.  

Are protein skimmers a filter?

Protein skimmers help to remove waste buildup (uneaten food, bacteria, algae, and fish waste) before they have the chance to completely break down and become nitrates and ammonia. They help to keep the aquarium water clean and healthy for your saltwater fish.

Common Types of Protein Skimmers and Things to Keep in Mind

Hang-On Skimmers (or HOB)

These skimmers hang on the back of your tank. They are a great option for tanks that do not use an all in one system and do not have a sump. These skimmers turn on and pump the water from the reef tank into its reactor column. The HOB skimming makes the same tower of foam and bubbles and collects the wastewater in its collection cup. However, these protein skimmers might be harder to adjust for variations in your tank and there can be a lot of hoses that might hinder performance if not properly cared for. Also if there is an overflow of water with a hang on, you run the risk of your floor or wall being covered in waste.


How these skimmers work is by placing the protein skimmer into the sump and raising it to the correct water height. When that is completed, these skimmers turn on and begin to use the water in the sump to create their air bubble collection which grabs the waste molecules hanging around in the reef tank’s water. These are the most commonly used protein skimmers and require a sump to function.  A great option for aquariums that are set up for LPS or SPS. The in-sump protein skimmers tend to be the most reliable and hardest working skimmers. They typically are more efficient in improving the water quality than hang on but that can be a subjective view. They do offer more control and thus can perform better than a hang on but that is not guaranteed. If there is an overflow of water, the excess water will simply fall back into the sump.

Different designs of Protein Skimmers


The original skimming design. used an open-ended tube with the base acting as the bubble source. This design used air bubble volume to bring bubbles and tank water together. The water flow is brought through the main chamber and the bubbles pop at the top of the chamber where the waste collects in the outer cup.


I am only mentioning this method to better explain the history. The counter-current design doesn’t work as well as the other methods. Essentially, the design calls for a much longer reaction chamber so that more waste can be collected but the size of the chamber is a little ridiculous. These designs inject water at the top of the reaction chamber and the air is injected at the bottom of the chamber. The design gets its name because, unlike the co-current design, the water falls towards the rising bubbles hence the counter-current name.


This style or design is really only defined by the type of valve that it uses in its design. The valve is called a Mazzei valve which doubles as an injection for both the waste carrying water and the air bubbles.

How to set up an in-sump protein skimmer

You want to identify the dimensions of the space that the skimmer would be taking up in your aquarium’s sump. The protein skimmer’s footprint is just the square dimensions of it, so you want to look at length, width, and then height to identify if you have the room for the protein skimmer. Look at the water level in the sump as well because if the skimmer does not sit in an appropriate level of water, you run the risk of an inefficient skimmer. There are skimmer platforms you can purchase to meet the height requirements, or you could jury rig your own platform if you are on a strict budget. The takeaway is that you need to be wary of measurements when deciding exactly what protein skimmer to purchase. Next, as with all new equipment purchases, you should give it a thorough rinse with water. You can use tap but depending on where you live it might be safer to wash the skimmer pieces in filtered water that you would be okay completing a water change with. After everything has been rinsed and assembled in the sump, open the skimmer outlet all the way to allow as much foam as possible to rise in the chamber. Now you wait. Yeah, you have to wait a couple of weeks as these skimmers begin to mature and lose the manufacturer oils that are attached to them but were missed during initial rinsing.

How to set up a protein skimmer without a sump

Okay, so you don’t have a sump, but you would like to have a protein skimmer for your tank. You are in luck there are models of skimmers that do not require a sump to function. Consider hang-on protein skimmers which, as you might expect, hangs on the back of your saltwater aquarium. You want to ensure there is room behind your aquarium for the model you are interested in first. Hang the skimmer, fill it with water and turn it on. It should begin to create its microbubbles to clean the tank.

How long do protein skimmers take to work?

Typically, protein skimmers will take about 2 weeks to be at their max effectiveness. Once it begins to create a consistent level of foam, you can consider it fully broken in. It also depends on how new your tank is. If your tank is mature, protein skimmers should begin working much faster than if it is a brand-new aquarium. As long as you properly maintain protein skimmers, they should continue to work for the foreseeable future.

How to tell if your protein skimmer is working

There are a few things to be on the watch for to decide if your new skimmer is working properly after its break-in period. The first thing to consider is anything in the collection cup. If organic waste is not being collected in the cup there could be several things to investigate. Double-check the pump and injector. You want to ensure that they are clean, and nothing is split or broken. Also, double-check your measurements. Is the skimmer in a water level that is too low? Remedy these issues and try again.

Foamy water overflow in protein skimmer

This is typically the cause of a skimmer that is not adjusted properly to its aquarium. Try to adjust the valves and height of your collection cup. If this does not work, consider what else might be going on in the main tank. Have you been adding anything to the aquarium that might be forcing the skimmer to overflow i.e. additives and certain foods? Remember everything is connected in a saltwater tank so thinking about the bigger picture rather than focusing solely on the specific problem could bring with it some revelations. Start with the problem and work outward.

No bubbles being generated when the protein skimmer is running

Typically this can be caused by a piece of the protein skimmer being dirty, broken, or improperly installed. Take the protein skimmer apart and see if everything checks out. Be sure to check the pump, air injector, hoses, and valves to ensure that nothing is wrong with the actual pieces of your skimmer body.

How to Tune your Protein Skimmer

First, make sure you checked the recommended water height that the manufacturer advised for the skimmer. You want to look at the manufacturer’s website to see if you are meeting all the requirements for the specific model of protein skimmer you have for your saltwater aquarium. There might be deviations that you need to account for with your protein skimmer. Many Protein skimmers come with adjustment valves that allow you to compensate for these measurements. Air bubbles and foam can be controlled using the drain and valves on the protein skimmer. But what do deviations in performance look like exactly and how do you tune for them?

A common problem is a dirty foam that looks like it is being removed from the tank but in all actuality can’t quite reach over the lip of the inner chamber preventing it from being deposited in the collection cup. What this means is that your protein skimmer is dealing with a lot of dissolved organic waste from your tank but is not getting enough air to whip of foam that will rise to deposit it in the collection cup. The waste then gets stuck in the reaction chamber and can cause a clog. To remedy this situation, you could raise the riser valve to increase the water inside the chamber to reduce the amount of foam being whipped up inside the chamber. What this will do will allow more of the foam to be picked up than before. Or add more air until the foam is regularly being deposited into the collection cup.

What if your protein skimmer is not picking up not enough compounds for foam production? The chamber will look more like it is boiling rather than whipping up foam. Either raise the water level inside the chamber like before to try to get the air bubbles before they pop. The problem with this is it not the most effective method and is more likely a temporary solution to your problem. Alternately, reduce the air injection through the protein skimmer by turning the air valve.  As with a lot of concepts related to saltwater aquariums, having a basic understanding of the concepts will allow you to better understand the tuning process.

How to Clean a Protein Skimmer

Cleaning your protein skimmer is vital for it to work effectively and efficiently for a long time. Remove the collection cup from the skimmer and give it a good rinse. The wash should consist of nothing more than a scrub and tank safe water. You are trying to remove the scum build-up that is present in the cup. This process should be done about once a week.

Protein skimmers should be taken apart and cleaned every 3 months. Soak the parts of the pump in vinegar to remove the buildup in the pump. The air pump and silencer should also be cleaned. Check semi-regularly to ensure they are not becoming blocked up over time.

Conclusion: Protein Skimming isn't for Everyone

Protein skimming is a great way to help ease your workload as an aquarist but you need to consider if it is even necessary in the first place. Hopefully, now you have a general idea if your reef tank will benefit from protein skimming as well as have a basic understanding of how the entire process works. The relationship of air, water, and waste bring about a system that deposits skimmate in a collection cup which you the hobbyist remove and clean. Protein skimmers work to improve the water quality in your reef tank through these waste-collecting bubbles. Protein skimmers work with your aquarium’s water quality since they need the organic waste to function at all. By understanding the core concepts of skimming, you set yourself up to avoid making common beginner skimming mistakes. Just remember that your main goal of skimming is to make your life easier, if skimming is not doing that there is something wrong.

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