quarantine tank setup

Quarantine tank setup – Saltwater Aquarium Blog

This post explains the need for a quarantine tank setup and provides a checklist to help you get started.

Why quarantine your fish?

Saltwater fish in the aquarium hobby are prone to injury, disease, infection, and parasites. The collection and transportation from the aquaculture facility or reef can cause damage and stress. The closed systems we keep the fish in are ideal for harboring and transmitting disease while lacking, at the same time, in the natural counter-measures which keep infestations in check in the ocean.

One infected fish can quickly spread disease or parasites throughout your tank and can cause a cascade of events that leads to devastating consequences. Once your display tank is infested, it can be a nightmare to get clean. You may have heard the expression: “an ounce of prevention is worth a pound of cure,” but in the saltwater aquarium hobby, an ounce of prevention is worth a kilogram of cure…which is 2.2x’s heavier than a pound.

quarantine tank setup

What does a quarantine tank do?

The quarantine tank, once set up, serves multiple functions. It provides a:

  • A physical barrier between your new saltwater fish and the display tank, preventing contamination in the first place
  • A way for you to closely observe and monitor the behavior of the new saltwater fish out in the open (most newly introduced saltwater fish will hide in the live rock or other ‘structure’ in your aquarium and only come out once they reach a minimum comfort level—which varies by species and individual)
  • A way for you to safely treat and remove any threats without the risk of harming any of your other livestock
  • ‘Recovery place’ for your newly purchased saltwater aquarium fish to eat, gain strength, and recover from the stresses of shipping and display at the local fish store—and get ready to compete for food and shelter with the other saltwater fish in your reef tank.

Quarantine tank equipment checklist

You don’t need a lot of fancy gear to set up a quarantine tank. The basic premise of a quarantine tank is that you want to set up a small, no-frills tank with separate equipment and water from your display tank. Here is all the equipment you need:

  • 10 or 20-gallon tank with a lid and light
  • Sponge filter (or other inexpensive, easy to set up filter, including hang-on-back style)
  • Air pump and airline
  • Aquarium heater
  • PVC Pipe
  • Timer
  • Surge protector/power strip
  • Preferred brand of aquarium salt (unsure which brand to choose? read more here)

I picked up a sponge filter and heater, air pump, and airline for just a few bucks on Amazon. Watch for sales at your local fish store. Stores around me periodically run a dollar-per-gallon sale every now and then, which is a great time to pick up a spare tank for a low, low price.

Step 1: Preparing the quarantine tank


In addition to the equipment listed above, you will also need a sponge (I prefer scotch Brite and magic eraser brands), but you can use whatever sponge you have available–as long as it is brand new as well as soap and chemical-free.Untitled-11

The first step in preparing your new quarantine tank is to clean it out. You don’t want to use harsh chemicals–or any chemicals at all if you don’t absolutely have to. Soak the tank for several minutes in clean freshwater to soften up any hard mineral deposits, and scrub it clean with your sponge. I prefer to clean my tanks outside, weather permitting) so I can splash around a bit and use the hose to fill the tank quickly.

If you have hard mineral deposits on the glass that won’t come out with a simple scrubbing, you can use a razor blade (if the tank walls are made from glass, NOT acrylic). The hard deposits should scrub right out. 

If you previously had an infected fish in the tank, consider disinfecting the tank with hyposalinity. Hyposalinity is a fancy term for a solution with a low concentration of salt. The best low salt solution is…you guessed it…freshwater.

Saltwater parasites generally don’t survive in freshwater, so run your tank for a few days with fresh water (after scrubbing it out).

Step 2: Setting up a quarantine tank

Setting up a quarantine tank is fairly straightforward. It is best to find an out-of-the-way location where your fish can gradually get used to living in your home. Go here for more information about selecting the best location.

  1. Place the tank on the stand.
  2. Fill it with saltwater.
  3. Place the heater in the tank, set the temperature (if needed) to 78 degrees F, and plug the heater into the power strip.
  4. Connect the sponge filter to the airline and submerge the filter in the water
    1. Squeeze the sponge to get out any bubbles and to help keep it from floating up
  5. Connect the airline to the air pump and plug it into the power strip
  6. Place a few short lengths of PVC pipe in the tank to give the fish someplace to hide
  7. Put on the lid
  8. Plug lights into a timer and then connect the timer into your power strip
  9. Go grab a snack


Step 3: Cycling

Just because you filled your quarantine tank with salt water doesn’t mean it is ready for your first saltwater fish. When fish are kept in an aquarium, they release a waste product called ammonia into the water. Ammonia is toxic and can burn or kill fish. Sometimes, this mysterious death is called new tank syndrome. To avoid new tank syndrome, you must cycle the aquarium before it is ready for your first fish. Be sure to cycle your tank and confirm the biological filtration is working properly before adding your first fish.

Selecting the best beginner fish for your saltwater aquarium is an important decision. You can learn more about that here. When you are just starting out, I recommend you avoid these fish.

Step 4: Adding first fish

Once your quarantine tank has completed cycling and you have picked out the perfect fish for your aquarium, it is best to acclimate the fish to your aquarium water before dropping them right in the tank. Place the new fish in a bucket or small plastic container and use a drip acclimator to drip water from the quarantine tank into the bucket. Once you have dripped enough water into double or triple the original volume of water, gently scoop your new fish out of the bucket and into quarantine using a specimen container (or similar plastic container).

It is also important not to add too many fish into the quarantine tank at the same time. 

Step 5: Monitoring your fish in quarantine

You want to monitor the fish in your quarantine tank for at least 30 days. 30 days is really the bare minimum and is still a little bit risky. If you have patience, you can wait even Untitled-9longer. Still, since parasites like saltwater ich have a lifecycle of about 28 days (depending on the temperature and a few other variables), you can have a reasonable assurance that the coast is clear if you monitor your fish in quarantine for a full 30 days and observe no parasites, or infected behaviors like shimmering, scratching, etc.

While monitoring your fish in quarantine, you also want to test the water to check ammonia, nitrites, and nitrates. If your tank is properly cycled and the biological filter is working properly, you should detect no ammonia or nitrites. If you test for and discover ammonia, take relatively immediate action and do a partial water change to lower the toxin concentration.


Periodically check the pH, temperature, and specific gravity to make sure the important reef aquarium water parameters are stable and normal in your tank.

Feed the fish with small meals a few times each day–take the time to watch the feeding closely to ensure your fish is active, healthy, and eating properly. Immediately clean up any uneaten food.

Visually inspect and observe the fish to look for parasites, cuts, scrapes, and any signs of injury or infection. If you see any damage or parasites, do some further research to investigate the recommended treatment option, like hyposalinity or antibiotics, and take the appropriate action. Please note that if you do detect a parasitic infestation, like saltwater ich, you have to start the calendar count-down over once you have rid your tank of the pest.

Record your observations

If you are going to properly use a quarantine tank set up, you have to be sure you maintain your livestock in quarantine for the full amount of time and are absolutely positive that the fish has had no symptoms during that time. The best method to help with this is to write down your observations daily in a journal. If you don’t record your observations, you run the risk of missing a day, forgetting what you saw, convincing yourself that you don’t have to wait for the full period (after all, 21 days is a long time…you would say to your future self) or any number of things which could end up invalidating the quarantine you did and could put your entire display tank at risk. Keep your recorded quarantine tank journal entries so you can learn and keep track of your progress.

Buy a reef journal here.

For more information

If it’s already too late and your fish are actively infected with a parasite, like saltwater ich, check out this article about treating saltwater ich. 

Or, if you want to know what to do when you are finished quarantine, check out this article.


Finally, if you are just getting started and want to learn more about setting up a saltwater aquarium, check out this article.

Watch this video about setting up a quarantine tank:


Written by Albert B. Ulrich III–author of The Reef Aquarium Series of books:  The New Saltwater Aquarium Guide, How to Frag Corals, 107 Tips for the Marine Reef Aquarium, and Reef Journal.

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