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Q11046 - HOWTO: How to Select, Setup and Maintain a Protein Skimmer by Keith MacNeil, Reef Squad member
Having worked in the aquarium industry for the past two decades (and then some), a question I often hear is "which protein skimmer should I get for my tank?"

Seems like a simple enough question. Truth is: it’s not.

There are literally whole chapters in books dedicated to this very question. Fortunately, we’ve read many of these books. Through our research and experience we’ve developed a deep understanding of all the various skimmer types available and what works best in different scenarios. With a little research and experience, you will, too.

This article should help you get off on the right foot.

To be clear: we are not going to declare one skimmer superior over another (check out the product reviews on our site for that). Our goals are to expose you to the different types of protein skimmers we carry, explain how to find the right skimmer for your aquarium and show you how to set one up and maintain it once you do.

AquaC Remora Hang-On Protein Skimmer

There are four basic types of protein skimmers available. Some skimmers, it should be noted, can be used in more than one application, meaning they can be used as a hang on OR in-sump skimmer (for example).

  1. Hang On Protein Skimmers
    As their name implies, hang on skimmers hang on the back of your aquarium. These types of protein skimmers are useful for aquariums that aren’t running a sump. The skimmer will conveniently hang on the rim of an aquarium similar to how a power filter hangs on to a tank. Generally speaking, hang on skimmers are designed for smaller aquariums (100 gallons or less). AquaC, CPR and Deltec are a few popular (and well-reviewed) brands on our website.
  2. In Tank Protein Skimmers
    In tank skimmers take up minimal space so you can place them right in your aquarium. Despite their slim size, they do an effective job removing organics from aquarium water. The most popular in tank protein skimmers are designed for nano aquariums. Check out the AquaticLife Mini and the Tunze Nano or Reefpack for examples.
  3. In Sump Protein Skimmers
    In sump skimmers are designed to sit within an aquarium system’s sump. It is within this sub-skimmer category you’ll find the most options available in terms of size and style. Prices range from a mere $40 all the way up to $3400, depending on your needs. AquaC, Deltec, Reef Octopus and ASM are prime examples of in sump protein skimmers.
  4. External Protein Skimmers
    External protein skimmers, as you may have guessed, run externally to the sump of your tank. Water from the sump is fed into the external protein skimmer. "Clean" water is then returned from the skimmer to the sump. If you’re in the market for an external skimmer, consider Deltec, Reef Octopus, Precision Marine Bullet or AquaC EV.
Eshopps S-150 Economy Cone Protein Skimmer
The main goal of all protein skimmers is to create very small bubbles within the skimmer to better attract dissolved organics. Different skimmers use different methods to produce these "micro" bubbles.

One of the most popular ways to produce bubbles in a protein skimmer is by using a venturi valve. Venturi valves use the force from water in the skimmer pump to pull air into the protein skimmer.

To "chop" incoming air into even smaller bubbles, some manufacturers include pinwheel or needlewheel impellers in their skimmer pumps. As bubbles pass through the impeller, "needles" or "pins" shred incoming bubbles into micro bubbles.

If your skimmer pump doesn’t include this specialized type of impeller, upgrades are available. Coralvue and AquaMaxx both make affordable needlewheel impellers for Sicce PSK skimmer pumps.

AquaC uses a patented technology called "spray injection" to produce the bubbles in their protein skimmers. Precision Marine uses a "beckett injector" in their line of Bullet skimmers. Air-driven protein skimmers are also available but have become less popular through the years.


If you’re not running a sump as a part of your aquarium system, you will need to decide between a hang on or in tank protein skimmer. Often the amount of space you have in/outside the tank is the determining factor for which type you’ll ultimately go with.

If you are using a sump, you’ll have your choice between all four types. Most sump users opt for an in sump or external protein skimmer.

You’ll want to take two important measurements before purchasing an in sump skimmer. First, measure the free space in your sump to ensure you’ll have enough room to accommodate the footprint of the protein skimmer you’re considering. Next, measure the maximum height you have available for your potential skimmer, taking into consideration the extra space needed to remove the collection cup. Knowing these measurements before you buy lessens the likelihood you’ll have to return the skimmer for another, more appropriately sized model.


Elos Natural Skimmer NS500 Protein Skimmer
While there are only four major types of protein skimmers, there are countless sizes and styles. To encompass all here would be difficult; we’ll instead hone in on the steps common between each type. We encourage you to follow the instructions included with your skimmer, if any. If you need help, contact us.
  1. Rinse your new skimmer thoroughly inside and out with warm water to remove any dust or residue left from manufacturing. If you’re using a hang on or external skimmer, you only need to rinse the parts that will have water in them.
  2. Place the skimmer in the appropriate location. Be sure it is sitting level. You may need to put some saltwater into the skimmer to help it sink (in sump) or before turning on the pump (some hang on models).
  3. If your skimmer did not come with the pump(s) preinstalled, connect the pump(s) to the skimmer inlet along with the feed tube (if applicable).
  4. Plug in the feed pump (if applicable) and adjust the water level within the protein skimmer.
  5. Now plug in the pump used for bubble production. Adjust the flow of air into the skimmer. Double-check the water level within the skimmer and adjust using the ball valve, riser tube or gate valve included with your protein skimmer.
Your skimmer should now be up and running. You’ll know it’s functioning properly if you see bubble production in the skimmer body. Keep an eye on your new skimmer for the next few hours to monitor its performance. You may need to raise or lower the water level inside the protein skimmer and increase or decrease the amount of air going into the skimmer for optimal operation. You may also raise or lower the collection cup. These little adjustments can make a big difference so don’t be afraid to fiddle with the settings. It’s almost important to point out many skimmers go through a "break in" period that lasts hours to weeks so you’ll want to keep a watchful eye on your skimmer, especially during these early stages.


The following steps are an excerpt from fellow employee Robert Farnsworth’s article, How to Clean Aquarium Equipment.
Tunze DOC Protein Skimmer 9020
  1. Turn off your protein skimmer and unplug the pump from the wall to avoid electrical hazards. Next, drain the skimmer in order to remove it from your aquarium, if applicable. Remove the pump and inspect all plumbing fittings for damage. Any o-rings or gaskets should be removed and inspected for cracks. You can apply silicone-based lubricant to extend the life of o-rings or gaskets before re-installing.
  2. Rinse the collection cup and skimmer body in RO/DI water to remove any sludge. Check venturi tubes and plumbing parts for any clogs. Rinse clean.
  3. Cleaning the pump is the most important part of this process. While the tips herein apply mostly to submersible pumps, external pumps are maintained much in the same fashion. First, carefully remove the impeller cover and inspect the impeller for any damage. Proceed to soak the pump and all components in vinegar, D-D Ezeclean or a similar solution in order to remove the calcareous buildup. I typically remove any sealing gaskets or o-rings before soaking. Take caution with impeller shafts as many are made from ceramic and can be fragile. Tooth or other small brushes are great for removing persistent build up and calcium deposits inside the pump.
  4. Finally, rinse all parts thoroughly in RO/DI water and reassemble the skimmer. Keep in mind you may have to let the skimmer "break in" again after cleaning the body and cup. Most skimmers require a little bit of time, often referred to as the "break in" period, to begin collecting adequate amounts of foam.
You should empty your collection cup weekly and clean it along with the protein skimmer neck/body to keep everything sludge-free. Even if your skimmer is equipped with a drain fitting for remote collection of skimmate, you should still clean the cup and body regularly to maintain maximum performance.

If you have any questions about protein skimmers, please do not hesitate to call (1-800-566-FISH) or write us. We can help walk you through skimmer setup if you’re stuck or make recommendations based on your individual tank specs. Our forum is a great place to talk to other reefers about what they’re using as well so if you’re not already a member, check it out. We’ve also included links below to related articles for additional reading.


Reef Ramblings: All About Skimmers by Adam Blundell M.S.
The Science of Protein Skimmers by Scott Brang
Protein Skimmers & Protein Skimming by Mike Paletta
Protein Skimming by Mike Paletta
How to Clean Aquarium Equipment by Robert Farnsworth
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Approved Comments...
it was ok for a novice , it did not go into great detail. That is good so as not to confuse a newbie. Approved: 3/31/2014
I always wanted to know how to choose the size pump for the skimmer? Is it a 4 to 1 ratio or less? If say I have a 90 gallon tank and a 30 gallon sump, how do I know how much skimming I will need or want to accomidate the 120 total gallons? Approved: 1/7/2013
I agree with the other comment about maintaining a constant water level in the sump. Also, the collection cup should be cleaned more frequently than once a week while the pump and body can go much longer than a week before cleaning is required. The initial break-in of a new skimmer notwithstanding, it is a myth that skimmer performance increases as it continues to run unattended. I believe most manufacturers recommend cleaning every 2 or 3 days. One other point is to consider how much a replacement skimmer pump costs. They can and do fail. Approved: 3/3/2012
Good basic instruction. Approved: 2/27/2012
Very helpful info.... Approved: 1/10/2012
I expected a deeper explanation of types and advantages among them Approved: 8/3/2010
When do I need a protein skimmer? some say I dont if Im only doing marine fish, not live rock or corals, but not sure. (editors note: Please send an email to for help with your question) Approved: 7/19/2010
Good usaboul info Approved: 4/8/2010
I felt it could have been more brand, and model specific. Approved: 3/23/2010
Too basic. I expected a better explanation of the fine tunning and a description of which type of skimmer is best for different type of acuariums. Approved: 3/22/2010
Didnt have much on adjustments and setup what level to set water and foam etc Approved: 3/21/2010
That was a great article, but missing a very useful piece of info. If you have a skimmer in your sump the water level in the sump has to be at the same level at all times or the pressure on the feed pump changes and the water level in the skimmer goes down. If you can put the feed pump in a chamber were the water level never changes it will save on alot of headaches. Approved: 3/21/2010
Great overall article by Kieth. It would have been nice to learn about some of the performance characteristics for the differant types since every manufacturer claims their design is the "best". Not looking for a "winner", just pros and cons of different systems maybe. Approved: 3/20/2010
Did not explain how to adjust it so it works the best. Thats the hardest part. To just say "set it up, turn it on, and adjust it doesnt help. Thanks anyway. Approved: 3/20/2010
Is a good article, I recomend a video to see how is done. Approved: 3/20/2010
Would like to see more info on in sump set up. Water level in sump, does it even matter? Etc. New to sump filtration and most of the articles are a little light on info. Not a bad read though. Approved: 3/20/2010
Good read Approved: 3/19/2010
Article Details
Created on 3/17/2010.
Last Modified on 3/31/2010.
Last Modified by Keith MacNeil.
Article has been viewed 37640 times.
Rated 7 out of 10 based on 89 votes.
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