How to Clean Protein Skimmer


How to clean protein skimmer? A vibrant aquarium usually becomes the focal point of every room. The small marine ecosystem in a tank with various fishes is a natural crowd-pleaser. It helps achieve that nice and calming ambiance.

Yes, it looks pleasing from the outside but is it clean inside too? The aesthetics are not as beautiful when the aquarium water looks dirty with unknown particles floating here and there.

Achieve clearer water by using innovative devices like protein skimmers. It is time to invest in a protein skimmer if you want excellent and clean water. Not only to showcase your fishes and plants but to have a more effective biological filtration.

What is Protein Skimmer?

A protein skimmer or otherwise known as a foam fractionator is a mechanical filter used to remove and clean organic compounds from water. These compounds can be uneaten food, bacteria, toxins from corals, and waste particles.

The primary goal is for the protein skimmer to end these components before they break down into nitrate and phosphate. When left untreated, you can expect algae’s growth and cause some health issues to your fishes and other marine species.

This is used commercially in public aquariums and water treatment facilities. At home, it can also be used to keep your saltwater tank clean.

Protein skimmers play an essential role in keeping your marine ecosystem healthy and safe.

Types of Protein Skimmers

In general, protein skimmers, regardless of type, work similarly. There are various developed designs, and some further improved over the years, tweaking the overall process.

Before knowing the differences of each of these protein skimmer types, it would good to understand how protein skimmers work.

Protein skimmers clean your aquarium but mixing huge capacities of small air particles into a column of water. The organic wastes, specifically protein, get attracted to the injected bubbles’ air-water interface, thus collecting on the bubble surface.

The organic materials that are not attached to the surface go up the column of water alongside the bubbles. It collects on the surface of the water as waste foam. This waste foam is called Skimmate, is then pushed up to the protein skimmer and then trapped in a waste collection cup to be thrown away.

Note that Protein Skimmers work best in saltwater. They don’t work with the same efficiency in freshwater because it doesn’t form the fine air bubbles that complete the process. Here are the different types of protein skimmers that slightly different work processes.

Counter Current Skimmer – for this type, the water is injected at the top of the water tube, and the bubble source and isolated fitting are set at the bottom of the device’s chamber.

The water, as the name suggests, would have to counter to the rising wall of bubbles. This is a top choice because it efficiently doubles the dwell time, increasing the protein skimmer’s productivity.

Downdraft Skimmer – one of the newer designs of the typical protein skimmer, this one is high and massive in design. It also needs a dependable pump so the air bubbles can be created.

The water is squirted at high speed in a tube that contains bio balls. Bubbles produced will then flow through these balls then traverse into a box where they’ll be pushed and gathered in the protein skimmer’s neck.

Compared to the other types, this is more costly to operate because it needs a powerful pump. The maintenance is also somewhat tricky.

Venturi Skimmer – this form of skimmer makes use of a venturi injection to produce air bubbles. This is achieved by drawing the air into its water stream.

This type is very reliable, and you can expect more power and an impressive quantity of foam. Additionally, since this skimmer depends on an exterior pump, you do not need to do frequent “tuning.” This is adjusting the level of water inside the skimmer’s chamber.

The only drawback here is the injectors tend to clog, so cleaning needs to be done regularly.

Aspirating Skimmer – this is arguably the top favorite among all kinds of protein skimmers. It is designed with the air being inserted into the impeller hole of your skimmer pump to generate bubbles.

The bubbles are then split into more delicate bubbles by a needle wheel, pegged wheel, or impeller.

Aspirating skimmers are designed small, so you can conveniently fit them inside the sump or under your aquarium stand. The installation is straightforward. It is economically friendlier to work since it just needs a low-powered pump.

How to Clean Protein Skimmer?

There is a misconception that your protein skimmer collection cup’s primary purpose is to collect all the skimmate.

It is the neck of the cup that plays a more critical responsibility in getting and pushing the waste up into the cup and out of your tank. When the bubbles are pushed up of the skimmer and into the neck area, the fewer struggles it encounters, the more seamless the process will be.

The main objective is for the bubbles to travel uninterruptedly over the rim of your collection cup. The bubbles should be intact so they can emerge as a skimmate. These bubbles are, unfortunately, too delicate. This is where regularly cleaning your collection cup comes into play because it affects the rest of the process.

When the cup is dirty, the bubbles would have difficulties sliding up to the neck and overflowing to the pooling area. There would also be lesser bubbles that can reach the cup because the bubbles would pop on the sides, leaving the wastes behind and splattered on the skimmer neck walls.

This overall defeat the very purpose of having a protein skimmer, so it is best to clean your mechanical filter twice a week. More cleaning schedules for your tank are needed, especially if it is bigger with more inhabitants because more waste is produced.

Cleaning is simple too and won’t take long. You also don’t need any special cleaning agents or tools to get the job done. Here are the three easy steps on how to clean a protein skimmer:

  1. Remove the collection cup from your protein skimmer’s body.
  2. Using warm water, rinse the collection cup and the neck. You don’t need to use any soaps, cleaning detergents, or chemicals.
  3. Wash away the wastes accumulated, especially on the inside of the neck, using a soft cloth or your hands.

Remember that even if you have the best protein skimmer available on the market today, its performance would still be affected if it is not clean and well-maintained.


How to clean protein skimmers? Protein skimmers are a must-have if you want your saltwater tank to have excellent quality water. This simple device alone can give your marine species a better chance of thriving and surviving because of the healthy environment that you set for them.

This is a smart investment, and with regular maintenance, you can ensure that it can keep your water tank cleaner for a good number of years.

With so many brands and kinds as your options, make sure that you choose one that can provide you with a reliable performance since it will be working 24/7, all year round. Do your research and check the protein skimmer that will suit your current set-up and meet your needs.

Leave a Comment