How To Set Up A Protein Skimmer

How To Set Up A Protein Skimmer

A protein skimmer is a key component in your reef’s filtration system and often one of the most expensive piece of equipment.
Are you planning out a new reef aquarium and have no experience setting up a protein skimmer or having trouble getting your existing skimmer to work properly?


Most reputable skimmer companies provide instructions on the set up and operation of their products. Start with that information when setting it up. But sometimes you will not find all the info you need.

Here is why we’ve created these additional helpful insider tips on how to set up and maintain protein skimmers so that you are sure to make it work correctly and easy.

Tips on tiny protein skimmers

The popularity of tiny reef tanks continues to grow.
With better LED lighting and
miniature water pumps, we can easily grow soft and SPS corals in the smallest of aquariums.
Thanks to forward thinking equipment manufacturers, even the smallest reef tank can have a protein skimmer!

These ultra small skimmers are powered by an aquarium air pump instead of a bulky water pump.
The idea was to make the
skimmer really small so it would fit in small reef aquariums.

These protein skimmers look like a thin glass or plastic tube.
The tube is mounted with a hanger or suction cup inside the tank. Microbubbles are created by a limewood air stone.

This old school method of running a protein skimmer with an air pump and limewood air stone is perfect for ultra small reef skimming.
Since there is no collection cup, skimmate flows from the top of the skimmer, through a hose, to a collection cup at the base of the aquarium.
This system works great but there are a few tips that make life with these miniature marvels easier:

  • You can position the skimmer anywhere on the aquarium but we like to place it on the back of the tank. This will help hide the air input line, skimmate hose and collection cup. Reef tanks just look better when hardware is hidden.
  • Don’t wedge live rock against the skimmer tube. Every so often you’ll need to remove the skimmer for cleaning and maintenance. Also, having a piece of hardware “stabilizing” a rock structure is a bad idea.
  • Air-driven skimmers will eventually form a salt crust inside the airline and fittings. This can restrict air in and skimmate out. The best idea is to completely flush the air adjustment and skimmate fittings with freshwater when cleaning the skimmer tube. Since the unit is so small, it’s easy to take it to the sink for a freshwater rinse.
  • Limewood air stones are great for making micro bubbles. Eventually they will plug up and cause back-pressure on the air pump. Keep a replacement air stone on hand at all times.
  • The small air pump needed to power the air stone works by vibrating a diaphragm. The vibration will make a humming noise. The better air pumps are relatively quiet. We like to place the air pump on a thick bath towel. The towel isolates the vibration from the floor or inside of the aquarium cabinet. Don’t cover the air pump! The electric magnet that causes the diaphragm to vibrate generates a little heat. Covering the air pump will trap heat and pump it into the aquarium.

Internal, In tank and HOB protein skimmers

All In One (AIO) reef aquarium systems
have simplified the set up of reef tanks by incorporating the filtration system into the aquarium.
Some All In One systems come with a protein skimmer, others make it optional.
The beauty of the integrated filter system is that it allows you to drop a skimmer right into the filter.
No plumbing or special installation is required.

If your All In One aquarium manufacturer offers an internal protein skimmer, it will be a simple plug and play operation.
In tank protein skimmers are designed to mount inside your aquarium with magnets or suction cups.
They’re normally placed in a corner of the tank or inside an existing All In One filter if the size is compatible.

Hang On Back (HOB) skimmers
are great for non All In One reef aquariums.
HOB skimmers attach to the aquarium just like a power filter.
Here are our tips for All In One, in tank and HOB protein skimmers:

  • When upgrading to a new AIO skimmer, check the dimensions to make sure it will fit inside the filter’s skimmer compartment. Check the height. Will it stick up above the aquarium and cause a distraction?
  • Internal skimmers come in a range of sizes. It may be tempting to over size an in tank skimmer but you’ll have to give up valuable aquarium space to make it fit.
  • Some in tank skimmers will fit inside an AIO filter system. Check the dimensions and the water in and out positions to be sure everything lines up properly.
  • HOB skimmers have plug and play simplicity but they take up space behind the aquarium. Some have a skimmer drain but all require periodic cleaning. Be sure you have ample space for maintenance.
  • Be careful to route the adjustment airline so it does not kink.
  • All of these skimmers are small in size, including the collection cup. The skimmer cup will need to be monitored every few days to avoid overflow situations.
  • Any hose or power cord is a potential source of drips and salt creep. Make a drip loop on all electrical cords. Wipe away salt creep every week to prevent build-up.

In sump protein skimmers

Big reef tanks need big protein skimmers.
For most reef aquarists this means placing the skimmer inside the sump. This configuration eliminates the need for external plumbing, cutting of holes and bulkhead fittings.
There are a variety of in sump skimmer designs and sizes.

You may even have a small reef tank with a small sump. In this case, you’ll be able to drop one of the smaller internal protein skimmers inside the sump.
For full size sumps you’ll have to decide which skimmer size, configuration and feature set works best for you:

  • Tall, narrow space-saving skimmers need to be “clamped” to the side of the sump. This keeps the skimmer stable and prevents tip-overs. Models with clamps make it easy to remove the skimmer cup with one hand.
  • Some in sump models place the submersible pump inside the reaction chamber to reduce the footprint. Check the dimensions to make sure it fits in your sump.
  • Aquarium stands have limited height. Place the skimmer where you will be able to remove the skimmer cup without having to tilt the entire unit.
  • Some DC water pumps come with a wired controller. Mount this unit away from water spray and salt creep.
  • Skimmer performance can change with the water level in the sump. Keep the sump topped off to maintain optimal performance. The manufacturer will provide specific water level recommendations for the model.

Final recommendations

No matter what size protein skimmer you select, it will require some time to “break in.” Residue from the manufacture of the skimmer inhibits the formation of foam and skimmate.
It can take three to four weeks before the skimmer is ready for fine tuning.
To reduce the break in period, rinse the skimmer with a diluted vinegar solution. Use 4 parts vinegar to 6 parts water.
This solution will rinse away residue and help stabilize foam production.

Every few months soak the skimmer in this solution to loosen organics and dirt from the skimmer components.
Take your time when making adjustments to your protein skimmer. After each adjustment wait a day to see how it affects the water level, foam production and skimmate.
Making drastic adjustments in short time periods will just prolong the set up period.
Once you’ve dialed in your skimmer, sit back and let it do all the work!

How To Set Up A Protein Skimmer