Fix a Protein Skimmer That’s Not Working |

Some people (wrongly) believe that if you want your fish tank to be clean, you can just add a protein skimmer that will do all the work for you. However, that is far from the truth: you actually need to actively maintain your protein skimmer. Without cleaning it regularly and replacing the media regularly, your protein skimmer can do more harm than good in many cases because removing some of your beneficial nitrifying bacteria.

How Does a Protein Skimmer Work?

how does a protein skimmer work?

It is a type of filtration system that is used to manage water quality in saltwater and freshwater aquariums. The build-up of waste, also referred to as dissolved organic compounds (DOCs), in the aquarium causes the water to appear hazy, sometimes considered an eyesore for aquarium owners.

A protein skimmer removes dissolved organic compounds before they decompose and release harmful ammonia and nitrite. The device is usually a porous cup or column which is connected to a water pump. When water is pumped through the skimmer, it goes into a thin air pocket. The air in the cup or column causes tiny bubbles to form, which carry small organic particles into a collection cup. A protein skimmer does not remove fish waste, which other filters remove, including filter socks, sponges, and pads placed in the aquarium. One of the most common reasons for a protein skimmer to stop working properly is that the water level has dropped too low or the waste clogs it.

Read : Suitable Protein Skimmer for Biocube 29

12 Reasons why your Fish Tank Protein Skimmer is not working

why is your protein skimmer not working?

Not enough space for water circulation

Have you ever asked yourself why the protein skimmer is not working? If so, you should know that there is a number of reasons that can lead to this situation. One of the most common reasons for that is that the protein skimmers “chamber” is too small or not in a good position. For your protein skimmer to work properly, it needs a lot of water circulation, so you should leave at least 10 mm of free space from the top of the chamber to the waterline.

The wrong type of protein skimmer

The most common problem that aquarists have with protein skimmers is that they are not working. Actually, the problem is that aquarists are using inappropriate protein skimmer. They are not using a protein skimmer that is right for their aquarium. The wrong protein skimmer cannot remove enough of the unwanted proteins, and the protein skimmer is not being used correctly.

Unsuitable air pump

If your protein skimmer is not working, it could be because of a problem with your air pump. This can happen if the air pump is not large enough to support the skimmer you are using. The air pump is the heart of the protein skimmer, and if it is running too slowly or is not sufficiently pressurized, it will not be able to pump the water through the skimmer, and the skimmer will not be effective.

problem with airline

You must maintain your protein skimmer correctly and set up a weekly or monthly maintenance schedule to clean the skimmer’s collection cup. If you happen to be using airline tubing, you will need to make sure that it is clean and free of kinks. If it is not, this may result in your protein skimmer not collecting enough waste, and the water may not be aerated enough to allow the protein skimmer to skimmate efficiently.

problem with water level

We all know that a protein skimmer is basically an air pump that creates tiny bubbles that cause water to fold over on itself, collecting waste and impurities in the bubbles. This is a helpful tool for your aquarium since the build-up of waste and impurities can lead to water toxicity, which affects your fish. Because of this, you need to make sure that your protein skimmer is working correctly at all times. You’ll know something is wrong if you notice that your water level is too high or too low. You can adjust the water level by using the skimmer’s adjustment knob, but you should only adjust the water level between half a centimetre and two centimetres.

Wrong-way to change air pump

Some of the time, it needs a new air pump to start working again. Usually, the air pump just burned out after extended use. If you have a protein skimmer that isn’t working, the air pump may be malfunctioning. The technical name for an air pump is a protein skimmer pump. These electric pumps are used to power an air-driven protein skimmer. Most skimmers that are not working have one of two problems: they either have a pump that isn’t working or have a protein skimmer that isn’t working because of a clogged air intake.

Improper installation

Improper installation of a protein skimmer is one of the number one reasons for having a protein skimmer that is not working. Many people purchase a protein skimmer and then they install it and wonder why it is not removing the organic waste from their aquarium. Most protein skimmers require specific installation, which will cause the protein skimmer not to work if not followed.

It is not cleaned up for a long time

If your protein skimmer is not working, it might be because it has not been cleaned for a long time. If you have not cleaned it for a long time, it will be clogged with debris and other visible particles that will block the water current in your protein skimmer, which is why it might not be working. Once this happens, you can still clean it.

NOTE: Be more careful when you clean the protein skimmer. You should not use bare hands to clean the protein skimmer. You need to use gloves when you are cleaning it. You may think that it is not necessary to wear gloves but this may be a cause to fish death by bacterial infections.

Improper air pump functionality

No matter how much you may have researched your protein skimmer before purchasing it, your protein skimmer is sometimes not working because of an improper air pump. Regardless of the type of protein skimmer you have, if your protein skimmer is not working, you need to do a little troubleshooting to find out why. Before making any adjustments, you should check to make sure the protein skimmer is connected properly, and the air pump is running.

Too much debris and dirt

Most protein skimmers have a filter that collects all the different things that go into the water. Sometimes, the visible debris or uneaten food that the skimmer collects can begin to clog the filter. As a result, the skimmer will not be able to pull out the necessary impurities from the water. When this problem occurs, it is important that the debris be removed from the water by changing half of the tank water.

you have not used the correct air pressure

The air pressure that is needed to run your protein skimmer is crucial. It is important to check the air pressure on your protein skimmer at least once a week to ensure that the skimmer is operating at peak efficiency. And if the air pressure is too low or too high, the protein skimmer won’t work properly. This is usually the cause of the problem. Checking the protein skimmer regularly doesn’t require a lot of work, so there really isn’t any reason not to do it. 

Irregular maintenance

Your protein skimmer is not working because of irregular maintenance. Not having performed the necessary tasks which are needed to keep it clean and well-functioning, you have made this device inefficient.

There are several problems that can be faced in case of irregular cleaning and maintenance.

As you know, a protein skimmer is a device that is used to remove proteins from aquarium water. Next to mechanical filtration, it is the most important device that you need to keep your aquarium water healthy and clear.

However, without regular maintenance, it will not perform its action accordingly and in time.

What To Do If Protein Skimmer is not foaming?

Protein skimmer is not foaming

If your protein skimmer is not foaming at all, it will not be able to remove any protein from your aquarium or pond. So, what do you do? 

The first thing you should do is check the collection cup, remove any solid debris, and then rinse it out and fill it with fresh water. Protein skimmers need some time to get up to speed, so let it run for several days before you make a judgment about it. If your protein skimmer continues to not foam, check the water level in the collection cup, as well as the skimmer.

What to do if your protein skimmer is overflowing?

protein skimmer is overflowing

A protein skimmer is an essential tool for keeping the water in your aquarium clean and clear, but it only works if it’s working. If the skimmer is overflowing, you’ll have to troubleshoot the problem before you can enjoy its benefits. One of the most common reasons a skimmer is overflowing is because of a calcium build-up inside the unit. The calcium blocks the water flow through the skimmer, causing it to overflow.

Here are the most common reasons for overflowing the skimmer:

1. If your protein skimmer is overflowing, first check the skimmer cup. It might be clogged, preventing the water from leaving the skimmer.

2. A dirty air pump may be the cause of it. A clean air pump improves the skimmer performance and prevents it from overflowing.

3. A clogged filter is also a common cause of a protein skimmer overflowing. Clean the filter to solve the problem.

4. Make sure your aquarium water level is not too high. If it is, then you need to use the siphon to drain the water.


I hope this article helps you find out the point why your protein skimmer is not working. If it is still not helpful for you, I recommend you to have a technician to solve your problem.

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