Does a Protein Skimmer Benefit a Reef Tank?

A protein skimmer benefits any reef tank by physically removing organic waste before it breaks down into harmful nitrates and phosphates. The result is clearer water, healthier corals, and reduced algae growth. If you’re new to reef keeping and wondering whether you need one, the short answer is yes — a protein skimmer is one of the most impactful pieces of equipment you can add.

There are many different protein skimmers to choose from, and the web is full of information that can make sorting it all out frustrating. Keep reading to understand the benefits protein skimming brings to your reef tank and what protein skimmer can be the best fit for your system. If you already know you need one, check out our guide on how to set up a protein skimmer.

What Does a Protein Skimmer Do?

Protein skimmers physically remove particulate and dissolved organics from the aquarium water. There are many different styles of skimmers, but all work on the principle of foam fractionation.

Inside the protein skimmer, millions of microbubbles are injected into the water. As the microbubbles rise inside the skimmer, dissolved organics stick to the bubbles and float to the top of the protein skimmer. This part of the skimmer is often called the “reaction chamber.”

The microbubbles burst and release the organics as a foam. The organic foam continues to build up and rise inside the reaction chamber. The goal is to create a frothy foam that is not too wet. Adjustments made to the protein skimmer help make the foam drier, containing less water and more organics. Fluffy foam continues to rise inside the chamber.

The foam eventually overflows the chamber and is collected in the skimmer cup. As the foam collapses, it collects as a liquid. This concentrated organic waste (skimmate) is a combination of tiny particles of organic matter, algae, and dissolved organic wastes. Skimmate can appear tan, brown, or greenish. The collection cup is periodically removed, cleaned, and replaced.

The concept behind protein skimming is to strip out the complex organic compounds before they can break down and release harmful nitrate, phosphate, and other pollutants.

Dissolved Organics in the Reef Aquarium

Dissolved organic compounds (DOC) accumulate in reef aquariums at levels hundreds or thousands of times higher than natural ocean conditions. Unlike a natural reef where tides flush waste into open water, a reef aquarium is a closed ecosystem with no automatic way to remove waste products.

Particulate and dissolved organic matter — including proteins, carbohydrates, oils, and fragments of dead plankton — builds up continuously. Algae cells leak internal organic fluids. Soft corals, LPS corals, and SPS corals produce organics and mucus. Saltwater fish periodically shed their slime coating. Millions of heterotrophic bacteria, phytoplankton, and other microbes float through the water, all adding to the organic load.

This organic buildup is one of the most important concerns for reef aquarists, and it’s the primary problem a protein skimmer is designed to solve.

What’s So Bad About Organics?

Excess dissolved organics in a reef aquarium cause yellow water discoloration, reduced light penetration, increased algae growth, and inhibited coral growth. In nature, reef ecosystems recycle organics through tidal flushing and complex biological systems. Reef aquariums lack these natural processes, so organic compounds accumulate and cause the following problems:

Benefits of Protein Skimming for Your Reef Aquarium

Adding a protein skimmer or upgrading to a more efficient model can result in measurable improvements in any size reef tank. Running a protein skimmer on your aquarium will provide the following benefits:

What Kind of Protein Skimmer Do You Need?

The right protein skimmer depends on your reef tank size and filtration setup. Protein skimmers are available as internal models for nano tanks, hang-on-back units for standard aquariums, and in-sump skimmers for advanced reef systems.

Nano and All-in-One Aquariums

If you have a nano tank or all-in-one aquarium, look for an internal skimmer. Many all-in-one aquarium manufacturers make protein skimmers that drop into their reef aquarium filter systems. This ensures the skimmer is perfectly matched to the aquarium. It will include a submersible water pump that pushes water into the skimmer and creates the microbubbles.

If you’re a DIY nano aquarist, a tiny internal hang-in-tank skimmer won’t take up much room. These are so small they can be run with an aquarium air pump. See our best nano protein skimmer reviews for top-rated options.

Larger Reef Aquariums

For larger reef aquariums, hang-on-back protein skimmers make installation easy. Just make sure you have room behind the aquarium for the skimmer. You may have to cut out a section of the light hood if you’re using a lid. For tanks 200 gallons and up, see our best protein skimmer for 200 gallon tanks guide.

Sump Filtration Systems

For reef tanks with a sump filtration system, you’re in luck. Most of the advanced protein skimmers are designed for use inside a sump.

Internal protein skimmers have a submersible pump that drives the skimmer and creates bubbles. The pump may be mounted inside the skimmer body, which takes up less space inside the sump.

Larger protein skimmers sometimes have the water pump mounted to the side of the skimmer body. This will require more room in the sump. Take measurements to be sure the sump and protein skimmer are compatible.

DC Powered Water Pumps

Many in-sump protein skimmers feature DC powered water pumps. DC current allows for more precise speed control of the motor. You can fine-tune and dial in the exact amount of water flow and bubble production.

DC water pumps make the adjustment process easy and use less electricity. They are very quiet and don’t cause vibration noise.

Drain Port Feature

Some skimmer models have a drain port in the skimmer cup. Just hook up a plastic hose and the skimmate will drain into a separate container under the cabinet. You can use a jar or plastic container to collect the skimmate.

This makes it easier to maintain the skimmer and reduces the frequency that you will have to remove the cup. The drain line also ensures the cup won’t overflow if you’re away on vacation or on a business trip.

Conclusion

Protein skimmers are considered an essential component of any reef aquarium. The results of continually stripping out organic pollutants are many. Your reef tank will stay cleaner and require less maintenance. Water quality will improve. You will see nitrate and phosphate levels decline.

Best of all, your corals and other sensitive invertebrates will grow faster and look more vibrant due to improved water clarity and quality!

Ready to get started? Our protein skimmer setup guide walks you through installation step by step. Browse more saltwater equipment guides to complete your reef tank setup.