Protein Skimmer Vs. Pond Skimmer (Which Is Better?)

By Matt Taylor  |  Equipment & Technology

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There are key differences between a protein skimmer and a pond skimmer for outdoor fish ponds. While these two devices have a similar name, and they both benefit the water quality of a fish pond, they work in different ways and serve different functions.

A pond skimmer is a necessary component of an outdoor fish pond as it filters the water. A protein skimmer, on the other hand, only supplements the filtration system, so it is optional but highly beneficial. Pond skimmers remove floating debris, while protein skimmers remove dissolved carbon.

Fish living in a pond produce solid waste in the form of fecal droppings. They also produce dissolved waste in the form of ammonia. Without a good filtration system, these waste products build up in pond water, reducing the water quality and causing algal blooms.

At excessive levels, ammonia is toxic to fish. Hence, a sound filtration system is essential for a fish pond. Here, we discuss two components of pond filtration systems – protein skimmers and pond skimmers.

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Protein Skimmers And Pond Skimmers – What Is The Difference?

When organic debris decomposes on the floor of a fish pond, it forms a layer of sludge. The microorganisms involved in the decomposition process use up a lot of dissolved oxygen in the water, leaving less for the fish.

If a layer of water in the pond becomes anaerobic (contains no oxygen), harmful bacteria proliferate and produce hydrogen sulfide. This causes the water to stink.

A pond skimmer mainly functions to remove floating debris from the surface of pond water. If leaves, uneaten fish pellets, and floating organic matter are removed before they have a chance to sink to the floor of a pond, it is enormously beneficial for maintaining good water quality.

A pond skimmer also reduces the need for frequent pond maintenance to get rid of the sludge on the floor of the pond.

Protein skimmers are fundamentally different from pond skimmers, but they also work to improve the quality of pond water and maintain a clear pond surface.

Protein skimmers are also called foam fractionators or bioprotein skimmers. They remove dissolved organic carbon compounds from pond water. This prevents unsightly pond scum or foam from forming on the water surface and prevents blooms of algae and blanket weeds.

Protein skimmers work by producing millions of tiny air bubbles. Dissolved organic carbon molecules are drawn to the air bubbles, so protein skimmers work to pull them out of the pond water.

Having low levels of dissolved organic carbon in pond water is good for the health of the fish, as it reduces their risk of infection and lowers their stress levels. This improves fish’s vitality and longevity.

Types Of Pond Skimmers

There are two main types of pond skimmers – floating skimmers and box skimmers. Both types of skimmers work to get rid of debris floating on the surface of pond water before it sinks to the bottom. However, box-style skimmers and floating skimmers have some key differences.

How Does A Box Pond Skimmer Work?

Box-style pond skimmers are designed to be built into a pond’s flat sidewall, and the box sits outside the pond. They consist of a weir door that sits partially submerged at the water’s surface.

Inside the skimmer sits a debris basket that catches large bits of debris, like grass clippings, fallen leaves, uneaten fish pellets, and small sticks.

Box skimmers have a separate compartment wherein the pond pump and filtration mats are installed. Box skimmers provide both mechanical and biological filtration.

The pond pump causes water to flow into the skimmer through the weir door. Larger bits of debris are mechanically removed by the debris basket. Then, the water is pumped through a series of filtration mats.

Beneficial microbes grow on the filtration mats. As water moves past the filters, the healthy bacteria convert toxic ammonia to non-toxic nitrate. The biologically filtered water is then pumped back into the pond.

How Does A Floating Pond Skimmer Work?

Floating pond skimmers are easier to install than box skimmers because they are not built into the pond's sidewall. They are great for ponds that do not have a straight edge.

This type of pond skimmer floats on the surface of the water and is connected to a pump with an adjustable flow rate that sits on the pond's floor. Some floating pond skimmers come with a built-in pump and filter mats.

Floating pond skimmers have a weir door that sits at the level of the water's surface. The pump helps to draw in water, so any leaves, twigs, grass clippings, uneaten fish pellets, and bits of floating debris are sucked in.

The debris is caught in a basket (which must be cleaned out regularly), and the mechanically filtered water is returned to the pond.

The Importance Of A Pond Skimmer

Having a pond skimmer is important to keep fish healthy inside a pond. Pond skimmers are essential for the following reasons:

  • They minimize the need for pond maintenance because they keep organic matter from sinking to the floor of the pond.
  • They maintain good water clarity, so the pond looks clean, and you can see the fish. This makes it easy to observe the fish and monitor pests and diseases.
  • They keep the pond water's surface free of debris and mats of algae.
  • They maintain optimum water quality through mechanical and biological filtration. This keeps the water well-oxygenated, ensuring that fish feed actively and grow rapidly.
  • They reduce how often filtration mats need cleaning, as they catch large bits of the debris before they get to the mats. This saves on labor and the cost of new filtration mats.

How Does A Protein Skimmer Work?

Protein skimmers, AKA foam fractionators, remove dissolved organic carbon compounds from fish pond water. This has the effect of preventing pond scum from forming on the water's surface.

Foamy pond scum forms due to high levels of dissolved organic carbon in the water. Plant debris, solid fish waste, and uneaten food that decomposes in the pond all contribute to dissolved organic carbon.

Protein skimmers work by producing millions of tiny air bubbles. These bubbles attract dissolved organic carbon compounds because of the structure of the compounds. One side of the molecule is hydrophilic (attracted to water), and the other is hydrophobic (repelled by water).

Protein skimmers produce bubbles that are the perfect size to attract these molecules. As the bubbles rise to the water's surface, the hydrophobic ends of the dissolved organic carbon compounds stick to the bubbles.

The bubbles holding the dissolved organic carbon compounds remain on the surface of the water, where they can easily be skimmed off and disposed of.

Does A Fish Pond Need A Protein Skimmer?

A fish pond does not strictly need a protein skimmer. But they are a very useful component of a pond, especially for people who are new to farming fish.

Experienced aquarists, like koi specialists, believe that if you feed fish the correct formulation of food in precisely the right quantities, the issues of high levels of dissolved organic carbon and pond scum can be avoided.

In aquaculture setups with an automated feeder that releases fish pellets in precisely the right quantities, a protein skimmer may not be necessary. However, if fish are being fed by hand, a protein skimmer will be advantageous.

The Advantages Of A Protein Skimmer

Many of the advantages of having a protein skimmer relate to the benefits of maintaining low levels of dissolved organic carbon in pond water:

  • In large ponds with water that is not circulated, a protein skimmer prevents the growth of surface algae, like a blanket weed, thread weed, and duckweed.
  • A protein skimmer prevents stagnant water from developing an unpleasant odor.
  • High levels of dissolved organic carbon can cause fish to behave lethargically and not feed as actively. Therefore, a protein skimmer keeps fish feeding and growing optimally.
  • Maintains high water quality, preventing the pH level from dropping and water conditions from becoming unstable.
  • Lowers fish's risk of developing ulcers and infections.
  • Reduces fish's stress and promotes their vitality

Alternatives To A Protein Skimmer

A protein skimmer isn't the only way to keep levels of dissolved organic carbon in pond water down. Certain materials can absorb dissolved organic carbon, and certain chemicals can be used to destroy it.

Materials that can actively absorb dissolved organic carbon are:

  • Granular activated carbon
  • Fine-grade montmorillonite clay
  •  Fine-grade zeolite

Granular activated carbon comes in a pelleted form and should be added to fish ponds. However, it only holds onto the dissolved carbon that it absorbs for a limited time, so the pellets must be removed before they release it back into the water.

Montmorillonite clay and zeolite have electrically charged particles that bind to dissolved organic carbon compounds. Together with the dissolved organic carbon, the clay or zeolite is then removed from the water via the pond’s filtration system.

Potassium permanganate is a chemical that neutralizes dissolved organic carbon. Adding 10 ml per 100 gallons of pond water will cause the oxidation/reduction potential of the pond water to increase rapidly. This destroys dissolved organic carbon compounds by oxidizing them.

Protein Skimmers For Large-Scale Aquaculture

Protein skimmers are not commonly used in small and medium-scale aquaculture operations due to the high cost of the equipment and its installation. A high-quality filtration system is often sufficient to maintain water quality in fish farms.

However, in large aquaculture setups with reduced or zero water exchange, floating protein skimmers are a key component as they maintain good water quality. They are used mainly for brackish tilapia production and the farming of bivalves, like mussels and cockles.

Big fish farms use cyclonic counter-current protein skimmers. They consist of an electrically powered air-water injector and two chambers housed inside a larger plastic cylinder.

With a high flow rate, they can process 26,000 gallons per hour. They create a strong current in a fish pond. Condensed foam is removed via a tube or hose, and the dried foam condensate can be used to fertilize plants.

Best Commercial Pond Skimmer

For a big aquaculture operation, the best choice of pond skimmer is one from the EasyPro Skimmer range. These pond skimmers are available in a range of sizes that can handle flow rates of between 3,000 and 18,000 gallons per hour.

These professional-grade pond skimmers feature a two-chamber design, so the pump can be inspected and maintained without taking out the filter brushes or debris basket.

Some models have an extension tube that allows installing the skimmer box and pond pump a further distance from the pond.

Best Commercial Protein Skimmer

An excellent choice of a protein skimmer for large-scale aquaculture is the MAT Protein Skimmer Filtration System. These protein skimmers come in various sizes, with flow rates of between 132,000 and 1,320,000 gallons per hour.

These systems remove dissolved organic carbon compounds that are less than 40 microns in diameter. They maximize dissolved oxygen levels in the water using ozone.

These industrial-size protein skimmers are energy efficient and have a low carbon footprint.


Pond skimmers and protein skimmers both serve important functions in fish ponds. While both these pieces of equipment maintain good water quality, they work in different ways. Pond skimmers remove floating debris from the water surface, while protein skimmers remove dissolved organic carbon from the water. It is essential for any pond to have a good pond skimmer.

Not all aquaculture ponds require both a pond skimmer and a protein skimmer. For example, in fish ponds with automated feeders that are well-calibrated, protein skimmers are not strictly necessary because there should not be a lot of uneaten food left to decompose in the water. However, for smaller fish farms where fish are hand-fed, protein skimmers can make a huge difference.

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