Protein skimmers are a vital part of a saltwater aquarium setup. They work by using small air bubbles and the properties of dissolved proteins, to remove these dissolved proteins from the water column. 

Having the best protein skimmer for your tank setup is as important as having a good aquarium filter, either a canister filter or HOB filter depending on the tank size, LED lighting, an aquarium heater, or any other essential accessory. 

Protein skimmers remove organic material which would otherwise break down and release harmful nitrogenous compounds such as ammonia, nitrite, and nitrate into the water column. Phosphate can also be released, which can be particularly problematic in saltwater tanks as it inhibits the uptake of calcium carbonate by invertebrates such as coral which uses it for skeleton formation and growth. 

Therefore properly cleaning and maintaining a protein skimmer is vital in maintaining proper functionality so that it can remain a vital cog in keeping your water clean and clear.

How To Clean a Protein Skimmer

How To Clean Protein Skimmer

A protein skimmer is composed of two main working units; the reaction chamber and the collection cup. Water is drawn into the reaction chamber where it meets a stream of fine bubbles. With reliance on some good old physics, the dissolved proteins and organic material in the water are attracted to and stick to the bubbles. As the bubbles rise it forms a foamy sludge called skimmate. This skimmate is then collected in the aptly named collection cup. 

As you can imagine, this skimmate leaves lots of residue which needs to be cleaned, and the collection cup needs to be emptied. 

To clean the collection cup, first things first, turn off the protein skimmer. If you leave it on there will be even more mess for you to clean up! Once the protein skimmer has become still, remove the collection cup. Be careful, and avoid spillage! Many skimmers have a release to easily remove the collection cup, while others are screwed on. Make sure to familiarize yourself with your skimmer.

Once the collection cup has been removed, you can discard the skimmate into the trash. Ideally this would be into something like a compost bin. It’s then time to clean the collection cup. You’ll need a soft sponge for this. There will be obvious residue which remains in the cup, and it needs to go. Don’t just use any household sponge, use a sponge that you save only for aquarium use. This is important, as any bleach or other household cleaning chemicals will cause havoc if it makes its way into the tank. 

In the same vein, to be careful you should use a bowl of aquarium water to scrub the collection cup in. Tap water contains dangerous chemicals such as chlorine which can harm the saltwater fish and corals in your fish tank.

When the collection cup is clean, give the reaction chamber a quick clean. If you have a large skimmer, you will be able to reach in and give the walls of the chamber a scrub with the sponge. The reaction chamber can remain installed where it is, such as in the sump tank. It only needs to be taken out for a deep cleaning every so often.

Once this is complete, then you can reassemble the skimmer and turn it back on. 

While this is how to do the basic cleaning of a protein skimmer, you will also have to do a deep clean. 

To do a deep clean, you will have to remove the skimmer entirely from the sump tank or wherever it is installed. 

Instead of simply scrubbing the collection cup and reaction chamber with a sponge, to do a deep clean and make coralline algae growth and any other hard to remove waste easier to get off you should soak them in vinegar solution. To make this solution you should dilute one part white vinegar with 20 parts water. Leave to soak until the encrusted dirt and algae has softened.  

Once it has softened you should be able to get the algae and encrusted dirt off with your aquarium sponge. If your protein skimmer body is too thin for your hand to fit in with a sponge, then buy a thin long handled sponge, or something else that can fit into the skimmer body. To maintain full function, you need to be able to get all the encrusted debris off.

Once you have fully cleaned the collection cup and the reaction chamber in the vinegar solution, rinse them thoroughly with clean water. Before you install them back into the tank, we recommend that you rinse the skimmer with tank or treated water, to prevent any contaminants from entering the tank.

When doing a deep clean of a protein skimmer it is recommended to also have a look at the pump and impeller. Check the pump for any dust and dirt that might be affecting performance. Coralline algae may grow on the impeller, depending on how the protein skimmer is manufactured. If there is any growth or buildup then soak and clean it as with the collection cup and reaction chamber.

How Often To Clean a Protein Skimmer

How often you need to clean a protein skimmer will depend on the size of your fish tank, the capacity of the skimmer, and the bioload of your tank. The bioload of an aquarium is the amount of living organisms that are living there compared to the size of the tank. Remember that everything, including fish, corals, and other invertebrates will all add to the bioload of your tank. The greater the bioload, the more dissolved proteins there will be in the water column, and faster the skimmate will build in your skimmer.

In general the collection cup should be emptied AT LEAST once a week. Usually the collection cup will need to be cleaned more often than this. If it is not emptied and cleaned this often it can overflow. If there is an overflow hose the extra skimmate will simply go back into the tank. This negates the skimmer, and it might as well not even be running!

Deep cleaning the entire skimmer, including getting all the encrusted growth in the reaction chamber, should be done at least every six months. If you can see that there is coralline algae growing and that the reaction chamber is getting very dirty in general then it should be cleaned.

There isn’t a real clear cut rule that you need to follow in terms of when to clean a protein skimmer. Get to know your skimmer and how it works with your tank. Then you will be able to clean it and deep clean it exactly as and when it needs it.

How To Clean Protein Skimmer Video

This is a great video which shows how to clean protein skimmers!

About the author

Authority Aquarium Staff

Authority Aquarium Staff writers are experts and aquarium enthusiasts, our in-house marine biologist fact checks all our content and reviews to bring you the best advice for your aquarium health.

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