How To Clean A Protein Skimmer Collection Cup

How To Clean A Protein Skimmer Collection Cup


This article will show you how to clean a protein skimmer collection cup.

In this comprehensive guide I will cover:

  • Why is it important to clean the collection cup
  • How to clean the collection cup
  • Tips to help clean your skimmer
  • Auto skimmer neck cleaners (ANC)
  • And much more


Protein skimmers play an important role in maintaining a healthy saltwater tank. They are an essential piece of equipment that you should use on your tank. As I mentioned in this article, they are not 100% required for keeping a saltwater tank but they are certainly beneficial in many ways.

In order for a protein skimmer to be as efficient as possible, it needs to be cleaned on a regular basis.

The collection cup of a protein skimmer will collect the skimmate being produced. However, the amount of skimmate and waste it collects it directly related to the neck of the skimmer cup. The neck plays a crucial role in getting the waste into the collection cup.



Why is it important to clean the collection cup?


When bubbles make their way up the skimmer body and into the cup, the less resistance they encounter the better. If the neck of your skimmer is dirty, the bubbles will encounter more resistance and less waste will be produced. Therefore being not as efficient as it could be.

The bubbles need to be intact as they reach the collection cup so they can “pop” and the foam waste can be collected.

If the skimmer neck is dirty, these bubbles will pop inside the neck and not the collection cup. This will keep adding to the film inside the neck and compounding the issue making it worse and worse over time. The neck of the collection cup needs to remain clean.

Have you ever seen skimmer cups and the necks of them are filthy with and muddy looking? Well, this is what you want to prevent from happening.

Although cleaning the neck of the collection cup is not difficult, it would be more efficient if the skimmate would collect in the cup as more waste could be collected over the same period of time.



How to clean the collection cup properly



In order to clean the collection cup, you need to remove it from the body of your skimmer. Then perform the following steps:

  1. Take the collection cup to a sink and pour the waste down the drain.
  2. Using warm water only, rinse out the inside of the cup and the neck. Never use soap, chemicals, or any other cleaning supplies as these are harmful.
  3. Wipe away and remove any waste that has built up on the inside of the neck. You can use a cloth, paper towel, pipe cleaner brush.
  4. Make sure the collection cup is clean and dry before installing it back onto the skimmer.

As mentioned above, cleaning the collection cup neck is very important. One thing to note here is cleaning a collection cup sometimes is not a pleasant job as the waste in the cup will be stinky and messy. Quite disgusting actually!

But by performing this essential maintenance task, it’s relatively quick and easy to do and greatly improve your skimmer’s performance and overall health of your reef tank.


How often to clean the collection cup


I mentioned how important it is to keep your skimmer cup clean on a regular basis. A good schedule to follow is to clean it at least 2 times per week. If your skimmer is producing more waste, clean it as you see necessary.

It may be required to clean the cup every two or 3 days but I find for the most part twice per week is sufficient.


Should you turn off the skimmer while cleaning?


It’s a good idea to turn off the skimmer for the few minutes it takes to clean the collection cup. If you have a hang on back protein skimmer, you do not want it overflowing onto the floor. In sump skimmers can be left on and then just remove the cup but then you risk it overflowing into your sump.

You also have the option to leave it running and just dial it down so the bubbles don’t reach the top of the skimmer. Then dial it back up when you replace the cup.

For me personally, I turn off the skimmer first then remove the cup for cleaning. I also use the ADJ PC100 A Power Bar, which makes it so much easier. Just use the rocker switch to turn on and off. No unplugging necessary. It also makes for a great upgrade for your tank. 



Tips to help keep your skimmer clean – maintenance


Not only is cleaning the skimmer cup essential, but you should also consider cleaning the skimmer body and pump as well. This will help improve the life of the skimmer and keep it performing at it’s best.

It’s common to see Coraline algae form in the body of the skimmer after a few months of use. This will be more difficult to clean versus the collection cup.

The skimmer pump should also be removed and cleaned of debris and deposits on the impeller blade and any other places it can grow on.



Here are some tips to help keep your protein skimmer clean:

  • Soak in a mixture of vinegar and water. Use 1 part vinegar to 10 parts water. This can help soften the deposits and makes algae easier to remove.
  • Scrub with a toothbrush or pipe cleaner brush then rinse.
  • Salt creep can be removed in hard to get at areas using a turkey baster.
  • Use a Rubbermaid container if you have a large skimmer.
  • Replace the air tubing as cleaning it is very difficult.

Plan to clean your complete protein skimmer at least every 6 months. You may need to clean it more often if you have a heavily stocked tank.

More tips on how to install and maintain your protein skimmer here.

Collection cup drain tube


Many skimmers today have a drain tube installed into the collection cup. It is used to drain the skimmate from the cup automatically and prevents it from filling up. Some people will attach a small bucket or container to avoid draining the cup all the time.

These tubes can be blocked from use easily using a cap that is provided with the skimmer. They can also be removed altogether if you don’t want to use it.

The collection cup drain tubes are great when first breaking in a new skimmer as they will generally overflow constantly for a while. The collection cups can fill very fast as the skimmer takes time to break-in.


Why is the skimmer cup overflowing?




There are many reasons why the skimmer cup is overflowing. If the skimmer is new to the tank, it’s common to see them overflow during the break-in period. Other reasons include:

  • Chemical Reaction – Skimmers do not like chemicals at all and they will overreact causing it to overflow. Certain chemicals like red slime remover, medications, epoxy putty, water conditioners, dechlorinators,  fresh filter socks, newly mixed salt,  bacteria additives as well as other dosing products.
  • Water level in the sump – It is important that you place your skimmer in the proper water level. The manufacturer will provide the operating water level you should use.
  • Blockage – The air intake could become blocked with debris, salt creep causing the cup to overflow. Also, make sure the air hose is not bent or too long preventing proper airflow into the pump.


Automatic skimmer neck cleaners (ANC)


Automatic skimmer neck cleaners are designed to automatically clean the collection cup of your protein skimmer to keep it running at peak performance. They are becoming more popular as they can reduce the amount of maintenance needed to clean the skimmer cup.

Automatic Neck Cleaners (ANC) will clean the neck of your protein skimmer and will reduce the build-up of waste. This build-up causes the foam to stick to the sides and can restrict the collection of skimmate in the skimmer’s collection cup.

Depending on the ANC unit, they will increase the height of your skimmer as well. You can check for different styles and prices by clicking the banner below.


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