How to Choose a Protein Skimmer

How to Choose a Protein Skimmer

Protein skimmers are an essential component of most reef-keepers toolkits and play a key role in removing waste and excess nutrients and keeping the water oxygenated. Before we discuss how to choose a protein skimmer, let’s go over the basics first.

What is a Protein Skimmer?

A protein skimmer, also known as a foam fractionator, is a filter designed to remove organic waste from the water column. The most common uses for a protein skimmer are municipal water treatment facilities, public aquariums, and home aquariums.

Protein Skimmer Parts
Protein Skimmer Parts

How Does a Protein Skimmer Work?

The protein skimmer pump creates microbubbles that push organic waste out of the water column and into the collection cup. Organic waste is hydrophilic and is attracted to the microbubbles inside a protein skimmer. As these bubbles rise inside the skimmer body, a foam develops that pushes the microbubbles and attached organic waste up into the collection cup. This process is similar to the process seen on a beach when the waves crash onto the shore. As the wave crashes, air mixes with the water creating foam and pushing the organic material onto the shore.

Protein Skimmer Process
Protein Skimming Process

Benefits of a Protein Skimmer

The primary benefits of a protein skimmer are waste removal and gas exchange.

Waste Removal: Skimmers remove dissolved organic compounds, including proteins and amino acids, produced by uneaten food, fish waste, and other biological processes. By removing these organic compounds before they break down, a protein skimmer helps prevent the formation of toxic ammonia, nitrite, and other toxic substances and helps control nitrate and phosphate levels. Protein skimmers can also help remove excess bacteria from the water column.

Gas Exchange: In addition to waste removal, a protein skimmer exchanges gas in the aquarium, replenishing oxygen back into the water column and removing the harmful carbon dioxide produced by fish as they breathe.

Do I Need a Protein Skimmer?

There are three primary factors when deciding whether or not you need a protein skimmer; tank size, type of tank, and type of corals.

Tank Size: Most nano-systems of 20 gallons or less do not require a protein skimmer as frequent water changes are generally sufficient for maintaining proper nutrient levels. It is also challenging to find a quality skimmer that will fit nicely on a nano tank. A protein skimmer is generally recommended for tanks 20 gallons and up.

Stocking Levels: Heavily stocked aquariums, including fish-only tanks, produce significantly more waste than lightly stocked aquariums and therefore have a considerably larger need for waste removal.

Types of Corals: Soft corals are much less sensitive to excess nutrients within the aquarium than LPS and SPS corals. Skimmers are generally still recommended for soft coral tanks, and they are must-haves for mixed reef tanks or SPS dominant aquariums.

Protein Skimmer Alternatives

While protein skimmers are one of the best ways to export nutrients from your aquarium, they aren’t the only way to do so.

Water Changes: One of the most straightforward ways to remove harmful organics from your aquarium is by performing regularly scheduled water changes.

Algae Scrubber: An algae scrubber removes excess nitrate and phosphate and converts them into energy for algae to grow within a confined space. 

Refugium: Like an algae scrubber, a refugium grows macroalgae that consume the excess nitrate and phosphate in the water.

Each of these methods is also commonly used along with protein skimmers.

In-Sump vs. External Protein Skimmers

How to Choose a Protein Skimmer: In-Sump vs. External Skimmers
In-Sump vs. External Skimmers

There are two common types of protein skimmers; in-sump and external. In-sump skimmers are significantly more popular than external skimmers. The chart below is a breakdown of the advantages and disadvantages of each type. In addition to in-sump and external skimmers, hang-on-back units are also available. Since their size is limited, hang-on skimmers cater towards smaller aquariums with smaller bioloads.

FactorsIn-Sump SkimmersExternal SkimmersExplanation
SpaceIf space is at a premium in your cabinet, an in-sump skimmer is generally the best option.
PerformanceBoth types of skimmers are efficient waste removers.
SafetyIn-sump skimmers are contained within the sump minimizing the chances of any leaks.
CostIn-sump skimmers tend to be less expensive than external models.
PlumbingExternal skimmers require additional plumbing to connect to the system.
DurabilityExternal skimmers are not submerged inside a sump, helping them hold up better over time.
HeatRunning an external skimmer removes the pump from the sump, thereby reducing any increase in water temperature.
Water Flow ControlExternal skimmers use a separate, adjustable feed pump to get the water into the unit.
In-Sump vs. External Skimmers

General Recommendations

  • An internal in-sump skimmer is wholly contained within the sump and is easier to set up, and is less prone to leaks.
  • Consider an external skimmer for very large aquariums and tanks prone to overheating.

Sizing a Protein Skimmer

Once you have decided on a type of skimmer, it is time to evaluate the size you need.

Water Volume: Most skimmer manufacturers provide a size range based upon the size of the skimmer and the air draw of the pump. As a general rule of thumb, stay towards the lower end of the size range. For example, a skimmer with a 100-200 gallon rating is best suited for tanks closer to 100 gallons, not 200 gallons.

Bio-load: Consider stepping up to the next size skimmer for tanks with a heavier bio-load.

Available Space: Many sumps have a small skimmer chamber; therefore, it is critical to measure your open space before purchasing.

Protein Skimmer Sizes
Protein Skimmer Sizes

General Recommendations

  • Measure the space you have to place a skimmer before purchasing.
  • Factor in both size of the aquarium as well as the expected bioload.
  • When in doubt, go bigger as it is best to have a slightly oversized skimmer than an undersized unit.

Additional Skimmer Features

While most skimmers operate in the same way, a good deal of innovation has brought plenty of new features. One of the most widely accepted changes to protein skimmers has been the migration towards DC pumps. DC pumps have allowed hobbyists to decrease their energy consumption while making the pump controllable. The controller enables the user to dial the water flow to the desired level and can temporarily turn off the pump to prevent the skimmer from over-flowing during feeding. Another helpful feature is a built-in waste drain on the collection cup. This drain directs skimmer waste to a collection container external to the sump.

General Recommendations

  • A controllable DC pump helps dial in performance and prevent overflows during feedings.
  • A built-in collection cup drain diverts waste to an external location.


In recent years, protein skimmer design and features have improved, and at the same time, they have become more affordable. In our opinion, a quality protein skimmer is a necessary component for all but the smallest nano-reef aquarium, and you no longer need to break the bank to get one. The Simplicity Aquatics line of protein skimmers features a DC controllable pump, a hybrid cone design, a needle-wheel impeller, and custom control to dial in the exact amount of skimming your system needs, all at an affordable price point. Quality second-hand skimmers are available for those on a tight budget; however, we recommend inspecting the unit in person before purchase.

General Recommendations

  • Choose a protein skimmer that is appropriately sized for your system. It is not worth saving money on a particular model if it will not meet the demands of your system.
  • If you are interested in a used protein skimmer, make sure to inspect it thoroughly and test the pump before purchasing.

Knowing how to choose a protein skimmer is essential. After selecting the proper protein skimmer, you will be well on your way to building a filtration system capable of meeting your tank’s needs. Like return pumps, regular maintenance on the skimmer pump and skimmer body will help keep it working well in the long term.

If you need help sizing a skimmer for your system or have any other questions about how to choose a protein skimmer, please contact our customer support team. And check back for future parts of our “How to Choose” series to complete your tank build.

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