How To Adjust A Protein Skimmer (Tips & Tricks)

Image Credit: Reef Tank Resource
Image Credit: Reef Tank Resource

How To Adjust A Protein Skimmer (Tips & Tricks)


A protein skimmer can make a huge difference in the quality of your water and really help reduce the water changes that you might need to carry out regularly. However, they can be a little tricky to set up if you are new to the hobby since they require a little bit of adjustment to reach peak skimmer performance.

Different Sized Protein Skimmers

30 Gallon Skimmer

For small tanks without a sump, hang-on skimmers are great.

65 Gallon Skimmer

Small tanks with a sump are better off using an in-sump skimmer.

100 Gallon Skimmer

Larger tanks need larger skimmers, but larger isn’t necessarily better.

150 Gallon Skimmer

Large skimmers are expensive and sometimes include adjustable pumps.

What do protein skimmers do?

First off, protein skimmers help to clean your saltwater tank by removing different waste particles and organic compounds by using foam to transport them outside the reef tank.  They do this by using air to whip up the water into a foam that travels up the protein skimmers tube. The waste actually covers the microscopic bubbles and the bubbles become the waste’s escorts out of the tube. At the top of the tube, the bubbles should pop and deposit the waste into the collection cup. It can be a really effective system when it is done properly but that’s part of the problem. A lot of new people don’t set up their protein skimmers properly and it results in waste either not being collected effectively or not at all.

Do you need a skimmer in a reef tank?

Like a lot of equipment for saltwater tanks, there are ways to get by without using a protein skimmer in your reef tank but they can make a big difference if used properly. If you decide that you don’t want to deal with setting up a protein skimmer, then it might be in your best interest to look into other methods of filtration to make up for the lack of a skimmer. However, if you can spare the cash, a protein skimmer can be one of the most time-saving pieces of equipment in your reef tank.

Can protein skimmers be too big?

Yes, in fact in the early days of the hobby protein skimmers came in very few sizes. What this meant was that the only people who could utilize protein skimmers were those with large tanks. It wasn’t possible to integrate skimmers into smaller reef tanks due to their bulk and lack of adjustment options. Nowadays, there are enough options within models that often there is a flexible range of aquariums that they can support but you still need to be mindful that your protein skimmer will fit well into your specific reef aquarium. 

You will need to get the dimensions of your reef aquarium or sump that you are trying to install the skimmer and begin to consider the different models and types that are currently available. A skimmer that is too big or small will not have peak performance. For instance, a new skimmer that is too big might not be able to whip up enough foam to even reach the collection cup; no matter what adjustments you try to make.

Installing protein skimmers

How you ultimately decide to set up your skimmer will depend on the type of skimmer and the type of aquarium setup that you are trying to implement.  Is your protein skimmer a hang-on design or does it go directly in your sump? The sump protein skimmers are in my opinion the cleaner design for looks as it places the skimmer in a place that is often out of sight out of mind but even these types have design variations. Instructions should come with your specific skimmer.

The different types all have their pros and cons so consider which one works best for you carefully before committing too early.  If you would like more information about each of these different types be sure to check out Reef Tank Resource’s article discussing the different types of skimmers and specifics on installing the various types.

The in-sump design is my favorite since it cleans the water in your sump before it returns to your aquarium for a more discrete setup.

How high should the bubbles be in protein skimmers?

The bubbles should be rising above the tube enough that when they pop or cascade the dirty skim water is placed in the collection cup. If your bubbles are too high you risk a dirty flood of bubbles splashing outside your aquarium and nobody wants that. However, if your bubbles aren’t high enough, your skimmer won’t be collecting the waste that it is supposed to be doing. The foam should bubble over the lip of the inner chamber into the collection cup.

You know if your skimmer is working properly if the collection cup is filling up with smelly dark skim. This is the waste that you are trying to remove. the average aquarium will take a few days to fill the cup.

How do you break in and adjust protein skimmers?

A break-in period is the first requirement and allows you to ensure that the skimmer is functioning as it is supposed to. If it is installed and issues begin to arise, you can quickly remedy them without any real issues arising. The actual break-in process is simply running the system and making tiny adjustments until it is perfectly set for your tank’s needs. Doing this will also help remove out any of the oils from manufacturing that you might have missed during your rinsing of the equipment.  Note that the general process applies to all models but there will be some variation in the exact way you might have to go about completing these steps. Review your skimmer’s guide to help identify the valves, knobs, and hoses that we will be referring to.  We are aiming for small bubbles that ultimately reach over the lip of the collection cup for depositing.

Step 1: Adjust the water level

Depending on the model of skimmer you have the valve will be different and will have a different level of nuance associated with it. A gate valve is preferable as it will give you much more control over the flow but you can manage with a ball valve. You want to adjust the flow until the bubbles are between the top of the tube and the bottom so the waste cup. Monitor your system and make tiny adjustments, as small as a quarter of a turn. Wait a few minutes to see what difference the adjustment made.

Step 2: Focus on the air being brought into the skimmer

This is less universal than the flow valve but somewhere there should be a knob or valve that helps to control the flow of air going into your skimmer. Managing the balance between airflow and water flow is the key to the water’s consistency and height within your skimmers tube.

Step 3: Ensure the skimmer is positioned correctly

There may be times when the skimmer was not placed in the correct water level in the first place which is preventing you from getting the performance that you are looking for. Make sure to review the skimmer’s manufacturer notes for specifics on the water level. Only do this after a few days of monitoring your system and making the other changes that were discussed. If you have done what you can with the other adjustments, then check to see if your model has a way to adjust its height built-in. If it doesn’t, you can make a platform to help raise the skimmer a few inches. These platforms are pretty easy and only require some PVC to create a platform. 

The actual break-in period shouldn’t take over a couple of weeks and once it’s done, you will have an efficient cleaning machine that will help to keep your aquarium sparkling.  However, it will also depend if you are working with an established aquarium or not. A mature aquarium will allow for a quicker break-in period.

How do you break in a protein skimmer with vinegar?

You can give your skimmer a vinegar bath to help break it in and remove a lot of the oils that covered it during manufacturing. It won’t necessarily speed up your break-in period but it will ensure that the oils are removed inside. To do this safely, you will need a large bucket and a few cups of vinegar. Set up the skimmer in the bucket with some tap water and pour the vinegar in and let it run for a day or two. Note that the skimmer will not run like normal during this process. Once the time is up, take the skimmer out and thoroughly rinse it.

Why isn't my protein skimmer bubbling?

Unfortunately, this is often caused by something being improperly installed or dirty. The best course of action is to take your protein skimmer apart and make sure none of your pieces are broken. You want to ensure that everything has been cleaned properly and that there are no cracks, chips, holes, or other issues that might need replacing. Cleaning the skimmer is relatively easy and you can just use some distilled water or other fresh water to rinse it out. You could even give it a vinegar bath (see the last section) to help clean it out.  If everything seems to check out, reinstall everything carefully to ensure that all the pieces are connected properly.

Should protein skimmers run all the time?

Once your aquarium has been fully cycled, you certainly could let your skimmer run all the time. The protein skimmer can make a huge difference when running all the time but you will need to watch for two things. Monitor the collection cup as it will fill up faster if the system is running all the time and make sure that the tank’s ecosystem needs that skimmer running. Depending on the needs of your tank, you might consider a timer (if yours doesn’t have one built-in). A timer will keep the skimmer running on a preplanned schedule so you don’t have to manually tune it every day.

Do you run protein skimmers while cycling?

No, there is no reason to run the skimmer during cycling as there isn’t anything to actually clean yet. In fact, there is a strong possibility that you will increase the amount of time your reef aquarium requires to cycle if it is skimming because it won’t be building that natural biology the way that is needed for a successful early tank. Let your protein skimmer rest until your aquarium has been fully cycled.

How do I stop my skimmer from overflowing the collection cup?

Before we can stop your skimmer from overflowing, we need to establish what the issue might be. 

  • If your skimmer is new, it might still be in its break-in period so you shouldn’t be too stressed about it overflowing. Follow the instructions for adjustments above and be patient. If after 2 weeks, you are still struggling to keep your skimmer from overflowing there is a different problem associated with it. 
  • Next, you want to tune your adjustments. Try to make the small adjustments that we discussed to the water and airflow. Maybe try to tune the height of the collection cup or reducing the speed of your pump. It will take a little trial and error but over time you will begin to recognize the nuances of your specific model of the skimmer.
  • There is also a possibility that the water could be the cause of the overflowing. Additives can sometimes cause overflow so if you have recently been using a water conditioner or other additive, it is possible that that is the cause. Stop using the product temporarily and see if there are any changes.

Final thoughts

The main takeaway is that you want to take the time to get to know your new skimmer. You have to break it in any way so work with the dials and tune it slowly over the course of those first two weeks. Watch the water level and foam height and you should be collecting skim in no time.

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