As a hobbyist, you've probably come across the term "protein skimmer" quite often. This remarkable piece of equipment plays a crucial role in maintaining a thriving reef aquarium by efficiently removing organic waste and harmful substances. In this blog post, we will dive deep into the workings of protein skimmers, explore their numerous benefits, and learn how to fine-tune them for optimal performance.

Understanding Protein Skimmers.

A protein skimmer, also known as a foam fractionator, is a filtration device designed to extract dissolved organic compounds (DOCs) and other undesirable substances from the water column of a reef tank. These substances, such as excess food, fish waste, and decaying matter, can break down into harmful compounds, causing water quality to deteriorate. Protein skimmers, however, work wonders in preventing this issue.

How Protein Skimmers Work.

Protein skimmers exploit the natural process of foam fractionation, which is based on the principle of surface tension. When the aquarium water is mixed with air, tiny bubbles are formed. As these bubbles rise through the skimmer chamber, they attract and bind to the DOCs and other waste particles present in the water.

The surface-active compounds in the organic waste tend to accumulate around the bubble surfaces, creating a foam that accumulates at the top of the skimmer chamber. This foam, containing the trapped waste, is continuously removed, leaving behind cleaner and healthier water in the tank.

Benefits of Protein Skimmers.

Improved Water Quality: Protein skimmers are highly effective in removing organic substances that can lead to poor water quality. By doing so, they reduce the risk of algae outbreaks and promote a healthier environment for your reef inhabitants.

Reduced Nitrates and Phosphates: As organic waste is removed before it breaks down, protein skimmers help reduce the accumulation of nitrates and phosphates in the water. High levels of these compounds can fuel aggressive algae growth, which is detrimental to the delicate balance of a reef tank.

Enhanced Oxygenation: The bubbling action in protein skimmers aids in increasing the oxygen levels in the water, benefiting the overall health of your reef inhabitants, especially fish and corals. The increase in oxygen can also help with increasing the PH level within the aquarium which is great for Corals, especially SPS. 

Clarity and Aesthetics: Regular use of a protein skimmer ensures crystal-clear water, allowing you to fully enjoy the captivating beauty of your reef aquarium.

Tuning Your Protein Skimmer.

To maximize the efficiency of your protein skimmer, follow these steps:

Set your skimmer at the correct water depth as per the manufacturers instructions. Turn the skimmer on and restrict the air going into the skimmer by simply placing your finger over the air intake to seal it. As the air bubbles leave the skimmer body you will see where the water level is inside the skimmer. Now use the water adjustment valve to raise or lower the water level to the neck of the skimmer where the cup attaches. Release your finger from the air intake and the skimmer body should once again start filling with air bubbles. Don't worry if the water level in the skimmer appears to drop, this is normal as air bubbles displace the water. Place the collection cup on top of the skimmer and large bubbles should start to form foam which will then rise up the neck and into the cup. 

Skimmers can take a while to react to adjustments so when you initially set it up, leave it an hour before making anymore adjustments. After an hour, see how it is performing. If there are foamy bubbles slowly filling the cup then great, leave it to do its' thing. If it's producing foam but filling too quickly then try reduce the water level inside the skimmer by opening the water level valve a small amount. Be warned though that skimmers take some time to break in so if it's overflowing rapidly, drain the cup into a separate bucket for an hour and see if the issue resolves. If not then as mentioned before, try opening the water valve. If foamy bubbles are forming in the neck but not getting in the cup then try increasing the water level in the skimmer by closing the water level valve. 

Another issue can be bubble production. Generally, if your skimmer looks like a boiling pot of water, lots of little bubbles popping as soon as they reach the top of the skimmer then you may need to allow more air into the skimmer. Some skimmers allow you to adjust the amount of air entering the skimmer. If yours doesn't then don't worry. Be aware though, skimmers can play up and bubble production can drop if you put your hands in the water or just after you've added food to the tank so before you begin making adjustments to the air intake, consider whether your skimmer is reacting to something you've done in the tank. If you think it is, then don't worry just give it an hour and see what it's doing later. As always, nothing happens quickly when adjusting or making changes with a skimmer. If your skimmer is producing really thick foam which isn't really collecting water in the collection cup then you are dry skimming and need to reduce the amount of air entering the skimmer. Waste water or 'skim-mate' in the collection cup should be the shade of a strong cup of tea (without milk). Adjusting the air intake is how we differentiate between wet and dry skimming. More on this below.  

Things to be aware of.

Keep in mind these few things as you set up and fine tine your skimmer:

Break-in Period: New protein skimmers require a break-in period of a few days to reach optimal performance. During this time, the bubbles generated will stabilize, and the skimmer will begin to remove waste effectively.

Water Level: Maintain the correct water level in the skimmer chamber. Adjust it as per the manufacturer's recommendations to achieve the best results.

Air intake: Some skimmers allow you to adjust the amount of air entering the skimmer. More air into the skimmer means the skimmer will produce a 'dry skim' whereas less air will mean a 'wet skim'. Wet skimming is generally better than dry skimming as it provides more opportunity for DOCs to be removed. The downside to this is that it removes a little bit more water so you will need to keep an eye on your salinity level. Skim-mate should be the colour of a strong cup of tea. Adjusting the air intake and to a degree, the water level will help you to achieve this.  

Collection Cup: Regularly inspect and clean the collection cup. This is where the accumulated foam is collected, and emptying it prevents skimmer inefficiency due to excess buildup.

Monitoring and Adjusting: Keep an eye on the skimmer's performance and adjust settings as necessary. Changes in tank inhabitants, feeding habits, and other factors may require slight adjustments to maintain peak performance.


Incorporating a high-quality protein skimmer into your reef tank setup can work wonders in maintaining water clarity, reducing harmful compounds, and promoting a thriving marine ecosystem. Understanding how protein skimmers function and fine-tuning them for optimal performance will ensure that your reef aquarium remains a mesmerizing slice of the ocean in your home. See the skimmers we have available on our website here or pop into the shop to see them in action. Happy reef-keeping!

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