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How to Set Up a Saltwater Aquarium Protein Skimmer

| Updated September 26, 2017

Things You'll Need

  • Distilled, or reverse osmosis water

  • Protein skimmer body

  • Airline tubing

  • Submersible skimmer pump

  • Measuring tape

  • Skimmer stand pipe

  • Drain plug

  • Utility knife (if needed)

  • Egg crate (if needed)

  • Plastic electrical zip tie (if needed)

  • Food grade petroleum jelly(optional)

A skimmer is an important tool for the filtration of a salt water, or reef, aquarium. The needle wheel style, in-sump skimmer consists of a plastic cylinder with a collection cup that is powered by a small, submersible pump. The needle wheel skimmer takes in air and mixes it with the aquarium water and forces this mixture into the skimmer body. This mixture is often pushed through a bubble plate, greatly enhancing the number of micro bubbles in the chamber. The skimmer filters as these small bubbles attach to proteins left over from dissolved organics in the water column.

Rinse out the skimmer body and cup with distilled or reverse osmosis water.

Attach the skimmer's airline tubing to the nipple on the skimmer pump intake.

Attach skimmer pump to the skimmer's inlet. Depending on your skimmer's manufacturer, this inlet may be located underneath the skimmer, or it may be a side outlet plastic pipe from the body.

Measure the waterline in the drain section of your sump. This is usually the largest section of the sump where the water from the aquarium drains into. Most skimmers operate at around 10 inches of water level. Consult your skimmer manufacturer for the ideal water level at which to operate your skimmer.

Measure the base of the skimmer.

Cut the appropriate pieces of egg crate into squares to build enough height needed to reach the desired waterline.

Stack the egg crate pieces together and secure with zip ties, and cut off any excess.

Place the skimmer into the drain chamber of your sump. If a stand is necessary, place the base of the skimmer onto the stand, inside the drain chamber, so that the skimmer stands upright.

Attach the skimmer stand pipe to the water outlet coming off of the skimmer's base and make sure the outlet portion of the standpipe is directed into the sump's drain chamber.

Attach the other end of the skimmer pump's airline tubing to the slide through on the body of the skimmer--or to the top nipple on the standpipe tower. Note: this end of the airline tubing must be exposed to the air for the skimmer to operate properly.

Seat the skimmer cup onto the skimmer body. For many types, the cup merely sits inside the inner seam on top of the skimmer body and light pressure is needed to seat the gasket. For most other types, the skimmer cup edge turns into a groove. For this type a small dab of petroleum jelly placed on the inside "track" will allow the cup to more readily twist on.

Place the skimmer cup top onto the skimmer and move side to side until the cup aligns with the grooves in the skimmer top. Note: this is a loose fit and not a seal.

Push the drain plug into the small hole on the bottom of the drain cup.

Plug the skimmer into a ground fault circuit interrupt outlet or power supply.

Watch the body of the skimmer as it fills with swirling bubbles. If the consistency of swirling bubbles is constant, and water is returning to the drain chamber via the skimmer's pipe outlet, then your skimmer is operating properly.


  • The skimmer may want to "float" in water until it is operational. Filling the skimmer body 1/3 to 1/2 with distilled water, or aquarium water, will prevent it from floating up off the base of the sump or stand.

    Upon start-up, give the skimmer a minute or two for the pump to achieve the proper air/water mixture. During this initial period the pump might be loud. Once a balance is achieved the pump should be fairly quiet and the skimmer body should be filling with bubbles. If the pump remains loud, unplug the pump and plug back in. Consult the manufacturer if the problem continues.


  • Risk of electrocution: When using electricity with the home aquarium, there is always the possibility of shock. For added safety, plug all aquarium equipment into a ground fault circuit interrupt outlet and use drip loops.

    Risk of flood: Make sure the skimmer standpipe outlet is directed into the sump.