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How to Set up a Quarantine Tank for New Fish (Step-by-Step)

While most readers of this site are convinced of the merits of an aquarium what about having a second tank as well? Only this tank will sit empty more often than not, be bare of decorations, and will usually house an unfortunate fish who is a bit unhealthy.

Interested yet? I’m here to discuss the merits of quarantine tanks and why you should always have one in reserve for the inevitable aquarium health crisis!

Why Should I Be Setting Up a Quarantine Tank?

Having a secondary aquarium that sits empty most of the time seems a bit counter-intuitive and even a waste of space and resources. However quarantine tanks are the best way to treat fish that aren’t at their full health.

In my experience, quarantine tanks have two major uses:

1. Treating Disease

When fish get sick most aquarists simply dose the entire aquarium and assume all is well. If your other fish are showing symptoms of especially contagious illnesses like Ich then a separate quarantine tank might not be warranted.

However treating a single sick fish is always preferable to medicating the entire tank. For starters, many fish are particularly sensitive to medications. Scaleless fish can be harmed by full doses of many meds.

And both fresh and saltwater invertebrates are notoriously sensitive to medications and can even be killed by them. Some agents are also toxic to plants while sparing animals.

Even your nitrifying bacteria can be at risk. If you use a broad spectrum antibiotic you may end up chemically sterilizing your substrate and filter of beneficial bacteria. This can result in an ammonia spike on top of your disease issues.

While medications are simple and usually effective they may not work in time to prevent a disease from spreading. Once you see symptoms in a single fish isolating the first instance will halt the spread of the disease and hopefully spare your other tank residents.

Lastly, treating fish in an isolated quarantine environment lessens the chance of selecting for medication resistance, particularly with bacteria. Dosing your entire tank may instead lead to an outbreak of an agent that no longer responds to the medication. In a quarantine environment even if this comes to pass the rest of your animals are safe.

2. Acclimating New Arrivals

Quarantine tanks are also perfect for new arrivals whose health may be compromised somehow. Wild caught fresh and saltwater fish have undergone an immensely stressful journey that often leaves them with the thinnest veneer of health.

They may have not recognized and refused prepared foods along the way, been crammed into crowded aquariums in subpar water conditions, and shocked by jolts and temperature shifts.

If these new arrivals suffer a sudden onset of disease then they are perfectly situated in a quarantine tank for treatment. Wild caught fish also often carry a heavy load of parasites that have taken their toll and need to be expunged.

New fish are also shy to feed or may not even recognize what you’re offering as food. If they are already stressed from transport and then have to struggle to orient themselves, feed, and fend off aggression from established residents…It can all lead to death.

Instead, you can provide a stable environment to monitor your new arrival while offering rich fresh and frozen foods to put weight back on them. You can also wean them onto prepared food if needed and even acclimate them to your main aquarium’s conditions over the course of days or weeks, as needed.

Lastly, a quarantine tank can also be used as a backup breeder aquarium for caregiving fish like Cichlids, for raising eggs and fish fry, or even raising Live Fish Food!

Items for 10 Gallon Quarantine Tank Setup

Here are some of the items you’ll need to set up a quarantine tank:

10 Gallon Aquarium

A 10 gallon tank is all that’s needed for the majority of quarantine purposes. It’s large enough to provide stable, clean water conditions for nearly any small or medium sized fish. Yet also small enough to dose without using too much medication or requiring much in the way of electricity or filtration.

For aquarists who need to quarantine larger fish a 20 to 30 gallon aquarium is preferable, depending on the fish in question!

Filtration Unit

While there’s nothing inherently wrong with a hang on the back or even canister filter for a quarantine tank, the majority of aquarists won’t leave a quarantine tank running forever. Not unless you’re constantly receiving new arrivals or treating sick fish.

Sponge filters are best because they set up quickly, they can be quickly inoculated with cycling bacteria, and they provide simple mechanical filtration. While most models lack chemical filtration like ammonia absorbing resins or activated carbon we actually want to avoid using these when setting up a quarantine tank.

This is because many chemical filtration media will pull out the medications we’re using to treat fish disease. That includes the activated carbon you’re using when dosing your main aquarium!

My favorite model is the UPETTOOLS Aquarium Biochemical Sponge Filter because it provides two places for bacteria to colonize. The initial sponge mechanical stage will provide surface area but the secondary ceramic media also provides a bacteria home while remaining free of clogging food or water particles.

UPETTOOLS Aquarium Biochemical Sponge Filter, Ultra Quite Aquarium Air Pump...
  • 【Multi-filtration Functions】Upettools sponge...
  • 【Special Ceramic Bio Filter Media】Upettools...
  • 【Removable Sponges 】 You can take down the...


Your heater can be on the small side; as a rule of thumb you need 3 to 5 watts of power per gallon of water.

However for setting up a 10 gallon quarantine tank the 50W version of the Eheim Jager is perfect. It’s affordable yet high quality and has enough power to keep your aquarium warm even if you have a cooler than average room temperature!

EHEIM Jager Aquarium Thermostat Heater 50W
  • Fully submersible
  • Thermo safey control protects against running dry
  • Will automatically turn off when water level dips...


Standard aquarium equipment. A simple liquid crystal thermometer allows you to monitor the temperature closely and ensure conditions remain stable. Since they stick on the outside of the glass you don’t have to get your hands wet unlike other styles that sometimes float away.

LCR Hallcrest A-1005 Liquid Crystal Vertical Aquarium Thermometer
  • Easy To Read
  • Mounts Vertically On The Outside Of Your Aquarium
  • Easily Movable

Aeration System

I recommend running an aeration system on any quarantine tank because boosting the oxygen content will help your fish heal. Sponge filters don’t usually provide as much surface agitation as other systems do.

Sponge filters do provide some aeration since they run on an air pump. However I prefer a dedicated secondary line powering an air diffuser. This means you’ll want a slightly more powerful pump than you’d normally use to drive both the filter and diffuser. A simple T-splitter along the line divides the flow equally and effectively.

UPETTOOLS makes a fantastic aquarium air stone that uses ceramic and a broad base to create an especially fine mist of aeration bubbles.

UPETTOOLS Aquarium Air Stones, Fish Tank Bubbler, Nano Silent Bubble Stone,...
  • 🐳🐳🐳 T150 Aquarium Air Bubble...
  • 🐳🐳🐳 Upettools Aquarium Air Bubble Stone...
  • 🐳🐳🐳 Noiseless Small Fine Bubbles Diffuse...

Cycling Bacteria

Cycling bacteria can come from several sources. The simplest method is to dip your sponge media directly into the filter sump of your established aquarium. Leave it there if possible for an hour or so and then add it to the quarantine tank.

It will have picked up some of your healthy cycling bacteria and they will eventually multiple as fish waste and leftover food accumulate.

If you want a larger, guaranteed dose of beneficial bacteria, you should instead use a cycling agent. API Quick Start is used precisely for this reason: setting up new aquariums and replacing lost bacteria from water changes!

API QUICK START Freshwater and Saltwater Aquarium Nitrifying Bacteria 16-Ounce...
  • Contains one (1) API QUICK START Freshwater and...
  • Allows instant addition of fish when starting a...
  • Reduces compounds harmful to fish when used...

General Purpose Medications

Lastly, I recommend keeping a handful of general medications on hand for common issues. Antibacterial and antifungal agents are necessary because every aquarist will deal with Fin Rot and other diseases now and again.

The only truly broad spectrum medication you’ll always want to keep on hand is aquarium salt! While it doesn’t necessarily kill off most infections (save through salt baths for some agents) aquarium salt stimulates the slime coat and improves gill function for freshwater fish. It’s also an excellent general tonic to be using in your main aquarium at all times.

API AQUARIUM SALT Freshwater Aquarium Salt 65-Ounce Box
  • Contains one (1) API AQUARIUM SALT Freshwater...
  • Promotes fish health and disease recovery with...
  • Improves respiration for fish in freshwater...

How to Set Up a Quarantine Tank

Quarantine tanks are meant to be bare bones and efficient in design. The above items are all you really need beyond essentials that go without saying like water dechlorinator, a hood, and fish food.

Even substrates like gravel and sand should not be used in quarantine tanks! Why? Because they are a barrier to cleanliness when they allow food and waste a place to get trapped. Water changes happen much faster when you can simply vacuum all of the debris up from bare glass.

I do recommend simple decorations like a single plastic plant and a cave, rock collection, or ceramic plant pot for fish to hide in or behind. A fish constantly exposed feels unsafe which has a definite impact on stress levels and both feeding and immune responses.

Subdued lighting is also best as it will encourage your fish to come out into the open more frequently where you can study it properly.

Always keep feedings light when a fish is in a quarantine environment, especially a tank that’s just been set up! Your beneficial bacterial agents may not be fully mature and certainly haven’t colonized the filter media fully. You don’t want to put a load on the system right away that could lead to ammonia and other toxic waste products building up.

A newly quarantined fish may not eat the first or even second day. It’s gone from a normal environment to one where there are no Dither Fish to let it know it’s safe. Expect it to be shy and to have a diminished appetite.

On the plus side if it eats heartily and looks for more you can be certain your temporarily impaired fish is well on its way to good health again!

How Long Should I Quarantine New Fish For?

This depends entirely on the fish and reason for quarantining it! Diseases like Ich or Fin Rot may take 1 to 2 weeks to run their course. Fin Rot and bacterial infections may take longer because even once the infection has stopped you’ll want to give your quarantined fish time for wounds to heal.

If you place your cured fish back into the main tank before their wounds are sealed they may get re-infected.

Quarantining wild caught fish usually takes 1 to 2 weeks, depending on the shape they arrive in. You’ll need to gauge their responses to live, fresh, and prepared foods, and wean them onto your meals of choice.

They may need to be treated for parasites and given time for missing scales and torn fins to heal. Lastly, the extra time allows you to adjust the quarantine tank’s parameters (which should match those of the pet store) to those of your main aquarium.

Long acclimations are especially important for wild caught saltwater fish and invertebrates because they come from environments that are significantly more stable and clean than most aquarium setups.


Quarantine tanks are very useful and not at all difficult to set up. And in exchange you have an isolated environment to treat the worst cases of disease and to allow new arrivals a chance to catch their breath. Setting up a quarantine tank is in the best interests of both you and your fish!

Jason Roberts
About Jason Roberts
Jason is an aquarium fanatic that has been a fish hobbyist for almost three decades.

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