How to Clean a Protein Skimmer & Collection Cup

Last updated on December 24th, 2022 at 11:04 am

If you are an aquarist, you must know how vital and necessary protein skimmers are in this industry. It is used to remove all the harmful and polluted particles from the water of aquariums. You can get an idea that the skimmer’s maintenance is essential for overall results.

The protein skimmers are just like a part of your aquarium, like any other equipment that gets dirty by the time. But also, when it gets aged, the skimmer becomes more sensitive, leading to absorbing extra dirt and waste in it. 

Regular cleaning helps a lot to avoid smell, bacteria, and dirt in the skimmer and tank. You have to clean it deeply after 5 to 6 months. For that, you have to take it out from the aquarium. It is the dirtiest part of equipment in your tank. That’s why it requires extra attention for its high maintenance and to keep the water quality safe.

Some multiple tips and tricks help clean it up without any major disaster or an issue in an aquarium. We have brought some exciting and highly effective methods to help you a lot in this case.

There are various sizes and types of protein skimmers, making sure that you are using the right choice for your skimmer. Otherwise, you may face some problems. 

Well, now, in this article, we are discussing the details regarding “How to Clean a Protein Skimmer.” There are multiple methods with a time limit from days to months; we have explained everything in the following. So, check it out below.

how to Clean a Protein Skimmer & Collection Cup

Methods of Cleaning a Protein Skimmer

Scheduling is a practical need to enhance water quality. The size is the most considerable thing of both the aquarium and the protein skimmer. It comes with a collection cup attached at the upper part of the skimmer, in which the entire dirt gets to collect from the tank. Over time if you don’t clean it up, there will be some notable smell issues. It also depends on the quality of your water. If it is not crystal clear but satisfactorily cleaned, cleaning the cup once a week would be enough. On the other side, if you own a giant size aquarium that would automatically get stinky would require cleaning daily or at least after every day.

A term known as skimmate proposes the dissolved material brought out from the water and collects into the collection cup.

Some severe bacteria, algae, fungi, etc., may cause difficulty cleaning the cup and skimmer. But if this isn’t the case and has standard waste productions, go for deep cleaning only twice a year. 

And if you want an instant rid from the fungi and all bacteria then unload all the water from the skimmer, unattached it from the pump for easy elimination of waste. For a more convenient process, the best trick would be to add some drops of vinegar to the water, let it soak and mix into it, then wait for some time. After, that uses a glove to remove all the waste by rubbing it off quickly. 

Better sanitization needs more effort, so make sure to wipe it off both internally and externally. Use some freshwater, rinse it in the skimmer, and then place it back in the tank. Only protein skimmer cleaning is not essential; focus on other attached pieces of equipment in your aquarium too. The cleaner environment you will encourage, the better results you will have: sensors, air pumps, water lines, etc. Don’t worry about them either; most of the procedures are the same and safe for them. Use vinegar here again to remove the green bacteria and germs from these types of equipment. You can use a scrub pad or brush to rub them off more efficiently, and the clear texture would come back.

Also, there would be some salt collected in your skimmer and aquarium both; for that, you will need to clean it every month because it minimizes the water quality. The primary fact is that it may affect the health of your fish and their environment. The turkey baster works like an excellent remedy, and you can use that as it eliminates the salt even from the bottom surface efficiently.

The scary thing is when water starts smelling, so take care of your products to avoid such disasters. Otherwise, it could be problematic and embarrassing.

We would suggest you a timely schedule for cleaning your protein skimmer for better and convenient procedures.

Methods of Cleaning a Protein Skimmer

Regular Cleaning:

The collection cup of the skimmer must get empty daily. Remove all the waste from it, rinse the cup through warm water, and then remove the rest of the bacteria or debris through the sanitizer wipes. There is a cylinder in the cup. Make sure to remove the gunk deeply from it. The other thing is to keep the sump water level in check. If you want to increase the performance rate of your skimmer, then make sure to maintain a standard water level; it helps a lot, like the changes in pressure can lead to some flexibility and significant changes in the protein skimmer and tank. But if the water level isn’t in control in the sump, you can add some device that will naturally increase the water level by adding some more into the pump.

Last, check the bubble needles or bubble setup to see if everything is going right or many adjustments are required. Make sure that the bubble needles of your skimmer must end at the upper point of the junction. Overall, it changes a bit from one tank to another or from one protein skimmer to another. 

Weekly Cleaning:

Weekends are preferred and the best days to serve your skimmer with more detailing; first of all, do not take the skimmer out. Just clean and wipe off the dirt from the neck and collection cup of the skimmer. Use warm water while cleaning it that helps to sanitize the products naturally and is entirely harmless. Try to use some soft material gloves or a cloth piece. Please don’t go harsh on it, be gentle and soothing with it. And if you don’t want to apply water while cleaning, then use wet clothing but make sure to eliminate all the unwanted material from both internal and external portions of your equipment. Also, while removing such things, remember to check if there is any leakage before tightening the boundaries and stoppers for reliable processes.

Related Info: How Long do Fish Live in An Aquarium?

Every 3 to 4-Month Cleaning: 

First thing first, detach it from the aquarium take it out. Open the skimmer, examine its parts and then start the procedure. After a reasonable time, the cleaning process must be efficient and detailed to be more durable and become easy to maximize its performance rate. In the process, first, you’ll need to detach the base plate, its cover and then put some vinegar into it. Fix a time, more than 24 hours would be perfect for eliminating and extracting all the debris, salt, and waste from it. After that, rinse it with lukewarm water and a soft hand; repeat the process on the same day if needed. Then wash venturi.

You will have to eliminate the venturi (it is the piece of equipment where the airline tube makes a connection with its motor) and wash both the internal and external venture portion, including the airline port on the side of the venturi with soft, warm water or you can use a bottle brush. If still required, then soak in a mixture of vinegar and water for instant results within 24 hours.

Tips for Cleaning Protein Skimmer:

Here are some quick tips conclusively for cleaning the protein skimmer.

  • Use turkey baster for eliminating salt rocks from the aquarium, placed in the skimmer. 
  • You can scrub off the dirt and stick particles by using a toothbrush and rub it off and rinse.
  • After some time, you should remove air tubing instead of cleaning it as extremely difficult.
  • Apply some water and vinegar all over the skimmer to remove bacteria or dirt layers.
  • If you are the owner of a big-size skimmer, we would prefer you to use Rubbermaid.

Cleaning of Collection Cup:

There are various methods that describe How to Clean a Protein Skimmer. We would suggest following the cleaning at least twice a week for your collection cup and pump to remove most of the waste regularly.

The best way is to remove the cup from the protein skimmer and then carry on the process. 

  • Remove all the debris from the cup.
  • Use lukewarm water to rinse the internal portion of the cup.
  • Do not use any powder, detergent, or chemical soap as it harms the stability of the collection cup.
  • Do not go hard with a cup; use a soft material glove, wear it on one of your hands, and gently remove it.

It is convenient and quick, but it is still challenging to clean the collection cup because all the dirt from the skimmer and aquarium has been collected in this cup.

Overall, after cleaning it on the days suggested, you will see a significant improvement in its quality and performance. 

Related Also: How To Get Rid Of A Black Beard Algae In An Aquarium?

Importance of Cleaning Collection Cup

Most people think that the collection cup is for only collecting skimmate. It plays a significant role while absorbing the waste from the aquarium. It is how all debris is collected and then goes out of the aquarium. When the collection cup is on its work, they prefer low resistance to perform better when the bubble flows up and transferring into the skimmer.

The aim is to transfer more bubbles towards the collection cup and as much as it can. The cup stored them as a skim mate. These bubbles are tiny and difficult to catch and control because of the dirt greasiness in them. The entire collection and resistance of these bubbles are only due to the cup, and making the cup clean and durable is your duty. So pop up the waste back quickly from the aquarium for longer life.

Importance of Cleaning Collection Cup
Should I clean my protein skimmer?

You only need to clean the body of the protein skimmer about every six months if the growth and accumulation are average. Coralline algae will ultimately turn your skimmer body pink. Wipe down the body of the skimmer inside and out. Then, rinse with fresh water and put it back in your aquarium.

How would I know that my protein skimmer is working?

You will know it’s working when you get a dry skim in the cup, and it will be very dark and smell bad. That skimmer cup should take about three days to fill up with gunk. If it is too wet, your cup will fill up fast, that’s not what you want, and you want foam of gunk going into that cup

Should protein skimmer run all the time?

Yes, it would work all day long, at least. If yours is a new skimmer, the pump could be broken. It can consume more than 30 days to break in thoroughly, and it usually quiets down once this happens.

Can I turn my protein skimmer off at night?

The pH level would drop a bit more during the night also if you turned it off. Skimmers work best at night, according to our experience.

Why are my filter-making micro bubbles?

If your outlet is placed above the water, the stream of H2 that flows down into your aquarium can trap air, pushing it underwater and producing the tiny bubbles floating around your tank. Then add extra water to your tank until the water level is in line with your filter boundaries.


As you have read the complete article on “how to clean a protein skimmer, we have given the entire tips and tricks, including multiple methods and importance. They all are natural and safe, so don’t worry about any one of them. Try to be consistent and follow the above guideline for the top-class protein skimmer in your tank.

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