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Best Protein Skimmer Options (Buyer’s Guide)

Filtration systems, including protein skimmers, are an important piece of aquarium equipment. They’re almost as essential as your reef salt selection. Not only do you want a beautiful aquarium with clean water, but you also need good water quality. This is the purpose of your filtration system. Using the best protein skimmer will make sure your aquarium is operating in good condition. Our favorite protein skimmer is the NYOS Quantum 300 Protein Skimmer.

Protein skimmers have been around a very long time and are frequently used in large tanks, public aquariums, aquaculture faculties, and fish stores. In this article, we’ll explore how protein skimmers work, what types of protein skimmers are available, and evaluate the best protein skimmers available for purchase.

What is a protein skimmer?

A protein skimmer is a type of mechanical filter that removes protein and other organic materials from the water. Examples of organic compounds include bacteria and toxins from corals, waste from animals, and uneaten food. 

The name protein skimmer comes from the filter’s ability to use the polarity of proteins to remove organic compounds from the water. It creates lots of tiny bubbles to which the proteins and other organic compounds stick to because of the polarity differences. Polarity differences essentially means the molecules have different electrical charges. Opposites attract so the protein molecules are attracted to the bubbles.

The bubbles then rise to the surface of the protein skimmer chamber, where the contaminants can be removed through a collection cup. You can skim the proteins off of the surface!

Protein skimmers remove organic compounds before they break down and compromise the water conditions. This translates to better water parameters for your fish. They can also keep algae under control, reduce nitrate buildups, and clarify your water until it is sparkling.

In addition to aquariums, protein skimmers are also used in industrial settings like municipal water treatment facilities. They’re an established and important form of filtering technology.

What is the best protein skimmer?

The best protein skimmer on the market is the NYOS Quantum 300 Protein Skimmer. It combines extreme performance, quiet operation, low power consumption, and easy maintenance as the best all-around option. However, you pay for the quality level so be prepared to spend money if you go this route. If you’re looking for nano skimmers, check out our nano skimmer guide. If you’re looking specifically for HOB skimmers, check out our HOB skimmer guide.

How does a protein skimmer work?

A protein skimmer works by pushing dirty saltwater aquarium water through a column of bubbles. The proteins and other organic molecules stick to the bubbles because of the polarity differences and the bubbles float to the top of the chamber. The bubbles burst when they reach the top of the chamber and the protein molecules then attach to and coat the sides of the collection cup. Ever so often, the aquarium keeper unscrews the dirty collection cup, dumps out the contents, wipes it clean, and re-installs it. Then the whole process starts again!

Types of Protein Skimmers

Internal Protein Skimmers

Internal protein skimmers are typically built for nano tanks. Typically, they use an air-stone to generate the bubbles. Because of this, the usual quality isn’t the best, although some high-quality builds do exist. Be sure to pay extra attention to quality and reviews if you’re looking for a skimmer for your nano tank.  

Hang-on-Back (HOB) Protein Skimmers

Like the name suggests, a hang-on-back protein skimmer (HOB) hangs on the back of your tank and pulls aquarium water directly out of the tank. They’re a good choice for smaller tanks that might not have a sump. However, they are usually not as powerful compared to in-sump protein skimmers. 

Aesthetically, they are also less attractive options as the pump needs to sit inside your tank, which can be difficult, if not impossible, to hide. 

In Sump Protein Skimmer

This is the highest quality category of protein skimmers. The best protein skimmer options operate inside a sump. It is common for reef tank owners to maintain a large aquarium sump that can hold these units (and other equipment). In sump protein skimmers have the most features like needle wheels or recirculation capabilities. If at all possible, we recommend purchasing an in sump protein skimmer for the best protein skimmer experience.

External Protein Skimmer

If you have a really large aquarium, you will likely be looking for an external protein skimmer. External protein skimmers are usually meant for larger aquariums (over 300 gallons) or commercial applications like aquarium stores or public aquariums.

Do you need a protein skimmer?

Protein skimmers are highly recommended for saltwater tanks, especially if you have a reef aquarium or you’re stocking with large or carnivorous fish.

In most aquariums, the main problem is keeping ammonia and nitrite levels low. The nitrogen cycle naturally turns these compounds into nitrates, which are non-toxic at low levels. However, corals are sensitive to the nitrates, which is why a skimmer is an important piece of equipment. However, you’re going to want to turn the skimmer off when you’re feeding the coral so they have an easier team consuming sufficient food.

Even if you’re a freshwater aquarist, a skimmer is still helpful. Skimmers can lessen the load on your filter system. If you have a functional filter system that is not quite enough for your tank, adding a skimmer can be a good option. Protein skimmers can also be made more efficient by introducing a biopellet reactor into your set-up.

A protein skimmer is an essential element of many of the filtration methods used by high end reefers today including the Berlin Method and Triton method

How to choose the best protein skimmer for your aquarium

Tank Size

Bigger tanks generally produce more waste. More waste requires larger skimmers. Buy a skimmer than can support your tank (or slightly more). Better to be slightly overpowered with your skimmer.

It’s also common for beginners to buy a starting tank, before realizing they want a bigger tank. Fishkeeping is addictive! Because of this, it is usually a good idea to consider buying up a skimmer size or two. You’ll be prepared for the inevitable upgrade!

saltwater aquarium using protein skimmer


Bioload is the amount of waste produced by the inhabitants in your tank. Therefore, bioload is determined by the amount and size of your fish. One 55-gallon tank will not have the same bioload as the next 55-gallon tank because of all the variables possible with inhabitants.

Little fish produce less waste than fewer large fish (i.e. puffers, eels, lionfish, groupers, etc). Larger and/or carnivorous fish produce a lot of waste so choose a bigger skimmer if stocking these species.


This one is simple. Your protein skimmer needs to be able to fit your space! Protein skimmers can be clunky looking, so also consider your aquarium stand space if that is an option too.


Not all skimmers are created equally and the price points will often reflect that.. Below are factors that will impact the cost:

  1. Features: Does it include a controllable DC pump? Can you control the bubble size?
  2. Quality: The equipment should feel sturdy. The skimmer has an important job in your tank and you want it to last.
  3. Support: Level of support from customer service is an important factor. A skimmer is a critical piece of reef equipment so you will want to make sure you’re using it right!

Don’t just buy the biggest option possible

Above, we recommend buying up a size or two on your skimmer. However, this doesn’t mean you should go crazy and buy the biggest skimmer out there. 

Although it’s difficult to over skim your tank, larger skimmers operate less efficiently. If your tank is too small to generate enough waste to create an ideal foam head it will reduce the efficiency of the equipment. 


Lastly, use reviews to help guide your decision. There are endless options out there but the wisdom of the crowd can be helpful in narrowing down your options. Reviews are also more helpful than ratings, as you can learn additional context behind the reviewer’s decisions.

Benefits of Using a Protein Skimmer

Protein skimmers have wide-ranging benefits for saltwater aquariums, including: 

  • Enhanced coral coloration from improved photosynthesis 
  • Improved coral growth due to improved photosynthesis
  • Better light penetration and sparkling clear water 
  • Faster recovery from fragging
  • Less algae growth
  • Less nitrates and phosphates in the water
  • Healthier fish

Best Protein Skimmer options:

There are lots of protein skimmer options out there. Now you’re educated on protein skimmers, let’s explore different options to find the best protein skimmer for your situation.

Best for Nano Aquarium: Reef Glass Nano Protein Skimmer

Nano Reef tanks can be challenging when it comes to purchasing a quality skimmer. Nano tanks are tiny to begin with so the aquarist is cramped from the beginning from a space point-of-view. The Reef Glass Skimmer is the smallest, effective protein skimmer on the market. It works on aquariums up to 30 gallons.

Because of its size, it is an air-driven skimmer. By design, it is not as powerful as a pump-driven skimmer. However, given the size and space restrictions, , this is still a great option. 


  • Needs to be paired with air pump
  • Height – 11″
  • Made of high-grade pyrex glass 


  • Affordable!
  • Fits in the smallest aquariums
  • Will withstand corrosive saltwater due to construction


  • Not pump driven
  • No waste collector

Best on a Budget:Bubble Magus BM-Curve 5 Protein Skimmer

The Bubble Magnus Curve series are great value protein skimmers. This is the protein skimmer that has been used by many reefers with great results. 

It is a practical, efficient needle wheel skimmer. It has a modern curve skimmer body, which is a common design in more expensive skimmers.

The main drawback of this skinner is that they take time to break-in (2-3 days minimum). Additionally,  the pump isn’t as heavy duty as some other protein skimmers on this list. 


  • Rated up to 140-gallon tanks
  • Height – 18.5″
  • Power Consumption – 8W @120VAC


  • Affordable
  • Lots of features from higher end skimmer models
  • Elite versions are available for those wanting better pump quality


  • 2-3 days to break-in at minimum
  • Pump quality is good, but not as strong as other models on this list

Best Overall: NYOS Quantum 300 Protein Skimmer

If you’re looking for the best protein skimmer, look no further. The Nyos Quantum is made in Germany. This skimmer has a pump designed for both power and silence, meaning you will have a beautiful and clean tank but you won’t know the skimmer is running. 

It is built with cleanliness in mind, so it is easy to disassemble for cleaning. This model also breaks in quickly, meaning you can enjoy immediate benefits. This is the best built needle wheel skimmer.

However, you will pay for quality as this is an expensive option. If you are looking for a very clean aquarium, this is your skimmer!


  • Made in Germany
  • Height – 20.9″
  • Power Consumption – 18W @120VAC


  • Top of the line performance
  • Easily disassembled for cleaning
  • Ability to create ultra-fine microbubbles


  • Expensive

Best for Aquarists who want more control: Aquamaxx ConeS In-Sump Protein Skimmer

The ConeS DCQ series can be dialed in to perfectly suit the needs of your aquarium. This skimmer uses the DC controllable Italian made Shark 2000 or 3000 engine, depending on the model selected. These skimmers work on gallons from 180 gallons to 480 gallons, giving them a huge versatile range. 


  • Italian made pump
  • Height – 19.3″
  • Pump power consumption: 25 Watts
  • Cell-cast acrylic construction


  • Shark DC needle-wheel pump produces optimum bubble size for high-efficiency protein skimming
  • Durable construction
  • Quiet – Rubber feet isolate noise and reduce vibration


  • Expensive

Reef Octopus Classic Protein Skimmer 

Reef Octopus Classic Skimmers are some of the original protein skimmers on the market. 

The Reef Octopus brand is well known in the industry. They became famous because they designed their very own pumps, versus using a protein skimmer with a pump bolted on that was originally designed for another purpose.

Reef Octopus also provides a 2 year warranty, which is better than the industry-average of 1 year warranty. 


  • For Aquariums up to 208 gallons
  • Height – 21″
  • Footprint: 10″ X 4″


  • Respected Reef Octopus name and quality
  • Skimmer pump is designed specifically for the skimmer
  • 2 year warranty


  • Price

Simplicity 240 DC In Sump Protein Skimmer

The Simplicity DC Protein Skimmers are an incredible value for DC (direct current) Protein Skimmers. These skimmers offer adjustable speeds and silent functionality, giving them high-end functionality at a reasonable price.

It is simple to use, which makes sense given the name brand. DC pumps also take less time to break in than traditional protein skimmers which means you’re up and running faster.

Simplicity is known for great customer service, so you can rest assured that you will be able to troubleshoot any issues you’re having.

Two things to note with this protein skimmer. The skimmer body is held together with nylon bolts so it’s not a quick release like some other options. Secondly, the protein skimmer pump is a re-branded Jabeo which gives us some concerns about the long-term durability.


  • For tanks up to 240 gallons
  • Height – 18.7″
  • Adjustable DC pump


  • DC powered pump = easy to adjust
  • Affordable
  • Good customer service


  • No quick release function for skimmer body
  • Jaebo Pump reliability

Protein Skimmer FAQs 

Can A Protein Skimmer Be Used in Freshwater Tanks?

Yes, protein skimmers can be used in freshwater tanks. However, they work much more efficiently in salt water. Freshwater lacks the ability to form the fine air bubbles that make skimmers efficient at removing organic compounds. 

Should I run my skimmer 24/7?

Most reef keepers run skimmers 24/7, only turning it off for very short intervals if nutrients drop below target levels. If this situation occurs, most reefers will turn it off for a night and then do a heavy feeding the following day, which usually gets things back on track relatively quickly.

Will A Protein Skimmer Reduce Ammonia?

A protein skimmer doesn’t directly remove ammonia. Instead, it removes organic compounds that decompose into ammonia then further change into nitrites and nitrates. This is how it keeps ammonia levels lower – by removing the compounds that can change into ammonia.

Do Protein Skimmers Remove or Reduce Nitrates?

Like ammonia, protein skimmers don’t directly remove nitrates. However, they help keep nitrate levels low by removing the organic compounds that decompose into ammonia, when then further changes into nitrites and nitrates.  

Protein skimmers reduce the load on the biological filter and can lead to reduced nitrates by removing organic molecules that would be broken down biologically, but your skimmer isn’t directly pulling any nitrates from the water.

Will A Protein Skimmer Help With My Algae Problem?

Yes, protein skimmers can help prevent the growth of algae in your aquarium. They do this by removing organic waste in your tank before it can be broken down into phosphates. Increased levels of phosphates are linked to algae issues and blooms. Phosphates are considered the “limiting nutrient” in aquatic ecosystems, meaning the available quantity of this nutrient determines the ability of the aquatic plant life to grow. In other words, more phosphates equal more plant growth.

Do Protein Skimmers Add Oxygen?

Protein skimmers do not add oxygen to tanks. They do not produce oxygen. However, skimmers do help with oxygenation of the water by mixing air and water. 

It uses the large surface area of the foam to allow oxygen to dissolve into the saltwater at atmospheric concentrations. Simultaneously, carbon dioxide also exits into the same air because of the amount of surface area. This process occurs at the rate that the air above the tank will allow (based on home indoor carbon dioxide concentrations).

How Often Should You Clean Your Protein Skimmer?

Cleaning frequency depends on the skimmer. Some do best with a totally clean neck, others seem to do well with some accumulated slime. Some reefers report cleaning the cup every few days, while others clean it out once a month. You want to avoid the cup overflowing back into your tank so it is better to be cautious with your cleaning.

If you’ve just purchased a new skimmer, we recommend cleaning the collection cup at least 2 times per week. If your tank is producing a lot of waste, clean it more often.  This will give you enough opportunity to better understand you skimmer and the ideal cleaning timeline.

Where Should I Put A Protein Skimmer In My Sump?

Put your skimmer in the chamber where the water level stays the most consistent. 

Should I run my skimmer while cycling?

Yes. The protein skimmer is designed to remove byproducts from the water column before they have a chance to be broken down by the microorganisms in your aquarium. 

If you don’t run your skimmer, all of these wastes will be converted into nitrates via your canister filter, live rock, and sandbed. Less waste in the water column equals less nitrates in the water column. 


Protein skimmers are a critical piece of equipment in saltwater and reef tanks. They are integral to clean water parameters, ideal coral conditions, and crystal clear water for improved coral photosynthesis and viewing. They help your tank stay a lot cleaner by removing organic waste products before they decompose into ammonia.

Our all-around recommendation for the best protein skimmer is the NYOS Quantum 300 Protein Skimmer. If you’re looking for the best protein skimmer on the market, this is it. 

Do you use a skimmer in your tank? What is your favorite protein skimmer?

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