How To Stop Microbubbles From A Protein Skimmer

For anyone setting up a new protein skimmer on your saltwater tank, you know how frustrating it can be to see all those microbubbles it produces.

It is very common for a protein skimmer to produce these microbubbles when it’s new. All protein skimmers including the hang on and in sump types can produce microbubbles.

Generally, they are not a cause for concern and they will go away once your skimmer settles which can be anywhere from a few days to a couple of weeks.

This article will explain why you might get microbubbles from your protein skimmer and how to stop them.

Why does a protein skimmer have microbubbles?

Microbubbles happen when a combination of air and water is forced out of the skimmer. Protein skimmers will normally create microbubbles for a few reasons.
The most common one being that the skimmer is brand new and it will take some time to settle in and perform properly.

Other reasons that a protein skimmer produces microbubbles:

Used skimmers that have not been used for some time.

If you set up a used protein skimmer that’s been sitting around for a long time, chances are it will produce microbubbles just like a brand new skimmer would.

Improper skimmer set up.

All in-sump protein skimmers will have a manufacturer’s recommended water depth where the skimmer should be operated. 8 or 9” water depth is common. If your skimmer is placed either in water that is too low or too deep, it will not perform properly and microbubbles will result. You can use a skimmer stand to raise the height of the skimmer inside your sump if needed.  

Improperly tuned skimmer.

It’s important to ensure your protein skimmer is tuned properly. Most protein skimmers have the option to control an air valve to find the maximum height of the bubble column. An improperly tuned skimmer will cause bubbles to exit the skimmer prematurely leading to microbubbles.

Chemicals, additives.

Many different chemicals can cause a protein skimmer to overreact causing the collection cup to fill rapidly and overflow into the tank causing microbubbles. This is very common and most products like red slime remover will recommend that you turn your skimmer off when using the product.

Overfeeding your fish.

Heavy feedings all at once or in a short amount of time can cause your skimmer to overreact creating microbubbles.

For the most part, these microbubbles will go away on their own over time.

You can prevent your protein skimmer from producing these microbubbles by ensuring the skimmer is set up and tuned properly, you are not using chemicals or additives, not overfeeding your fish, and simply waiting it out if the skimmer is new.

How to stop microbubbles from entering display tank

If you want to prevent microbubbles from entering your display tank, there are a few things you can do. If you are using a hang-on style of skimmer like the Reef Octopus BH2000, it will come with a few sponges that fit over the return tube which will trap the bubbles leaving this skimmer.

This can drastically reduce the amount of bubbles entering the tank. Normally you can remove the sponges after a few days once you notice the microbubbles have stopped. 

If you have an in-sump skimmer, you can position the skimmer in a different location where the microbubbles can dissipate before reaching the return pump section.

If possible, position the skimmer against a sump divider so when the water exits the skimmer, the bubbles will be forced up the wall and dissipate at the water surface before being returned to the tank.

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Are microbubbles harmful to a saltwater tank?

No microbubbles are not harmful to a saltwater tank.

There are many discussions about this topic throughout the saltwater aquarium community. Many people will disagree and believe that microbubbles are harmful. There is no evidence of this that I have seen.

Small bubbles are very common and natural in reefs around the world. In your saltwater tank, there are pieces of equipment like powerheads and wavemakers that produce microbubbles on a consistent basis.

These bubbles get sucked into filters and protein skimmers causing even more microbubbles.

Other than being an eyesore, microbubbles are not harmful.

How to tune a protein skimmer

As mentioned, if your protein skimmer is not tuned properly, it can produce microbubbles. Here is a great video that shows how to tune your skimmer properly.


The most effective way to reduce microbubbles from your protein skimmer is to simply wait it out. It just takes time for a new skimmer to adjust to your tank. The bubbles are harmless and won’t hurt anything. But if you want to reduce them faster than waiting it out, try the methods mentioned above. If the bubbles are caused by adding chemicals, consider turning the skimmer off as recommended and the bubbles will go away.