How to Quarantine Fish the Right Way

Sometimes, you may need to separate new, sick or injured fish. It’s a good idea to quarantine new fish from your established fish to ensure the newcomers aren’t bringing in harmful bacteria, viruses or parasites.

It can happen that fish look perfectly fine when you get them, but then a week later, they’re covered in ich and spreading it to your healthy, established fish. 

Or you might have an established fish that comes down with an illness or has been injured by a tank mate.

In all of these cases, quarantining fish is your best bet to keep problems from spreading through your display tank.

However, setting up a quarantine tank isn’t as simple as filling a spare tank with water and throwing fish in it.

But, no worries. Today, I’ll go over some strategies and tips for successfully quarantining your fish.

How to Quarantine Fish the Right Way

Goldfish swims in quarantine tank

The Aquarium Nitrogen Cycle

In any aquarium system, fish and invertebrates put out feces and urine that can build up and produce toxic ammonia. If enough accumulates, it will kill all of the livestock in the tank.

Aquarium filters house beneficial bacteria that eat this ammonia and ultimately transform it to nitrate, a substance that is not harmful at low levels.

However, it can take weeks for enough of the beneficial bacteria to colonize the filter, and make the tank safe for fish in a newly set up aquarium.

If you are not familiar with the Aquarium Nitrogen Cycle, I would highly recommend that you view our in-depth article, here. The rest of this article will be written in a way that assumes the reader is familiar with this process.

The Big Problem with Quarantine Tanks

Making sure that your quarantine tank is properly cycled when you add fish, especially if you have to add fish in a hurry, can be a major problem. 

You don’t want your quarantined fish to be stressed or killed because of ammonia spikes in the tank.

Even if you cycled your quarantine tank, if it just sits there empty, the lack of fish waste will starve the beneficial bacteria and they’ll all die; this will set you back to square one. 

The best solution is to add some seasoned filter media from your existing tank when you add your fish. 

Large numbers of beneficial bacteria will ride from the display tank to the quarantine tank on the biomedia, jumpstarting the cycle.  

Be Prepared

My number one recommendation, if you know ahead of time that you’ll be buying and quarantining fish: set up a sponge filter in your main display tank a few weeks (a month is even better, if you can) prior to buying your fish. Let the filter run in the existing aquarium, it will get colonized by beneficial bacteria that live in the display tank.

You can then transfer the sponge filter to your quarantine tank when your fish arrive. This seasoned filter will be able to immediately process fish waste without having to go through a lengthy cycling process.

Another way is to remove some (but not all!) of the biomedia from your main tank’s filter and place it on or in the filter of your quarantine tank.

In a pinch, you can even place an airstone underneath mesh bags of biomedia. The air bubbles will push water through the media, providing food and oxygen to the beneficial bacteria. 

Disclaimer: There is a small risk of cross contamination if you use seasoned filter media from your existing tank. If there are sick fish in your display tank, harmful pathogens can ride from one tank to the other. However, in my opinion, the benefits of having a ready source of beneficial bacteria far outweigh the risk in this situation. 

Setting Up a Quarantine Tank

Rule number one with this, quarantine tanks do not need to be fancy. In fact, if you’re separating sick or injured fish, a bare bones tank is much easier to care for.

Tank Size

I normally recommend that people get the largest possible tank they can afford to house fish. The phrase, “bigger is always better,” gets thrown around a lot.

But, that’s for display tanks, meant for long-term housing. 

Quarantine tanks are meant to be temporary housing for new or sick fish. 

You don’t have to go all out on a huge tank for quarantining. You can usually get away with the minimum tank size for the species of fish you need to separate.


The best filtration for a quarantine tank, in my experience, is air driven sponge filters.

They provide excellent aeration, as well as mechanical and biological filtration, and they are cheap and easy to use. 

I love that they provide a really gentle current that’s good for even delicate baby fish.

Please, see our sponge filter article, here.

You can use other kinds of filtration, if you want to, of course, like hang-on-the-back or canister filters. 

I just recommend that you go with a gentle current that won’t overwork already stressed fish. And make sure you’ve got lots of room for biomedia.


I recommend that you don’t add any substrate to your quarantine tank. It is much simpler to remove solid waste from a bare bottom tank. This will help you keep nitrates to a minimum.

Sure, it doesn’t look as nice, but we’re more worried about function than aesthetics in this case. 


Again, no need to spend the money on expensive lights for a quarantine tank. You only need enough light to see your fish clearly so you can monitor how they’re doing.

Cheap LED lighting will be just fine.


Whether or not you need a heater will depend on what kind of fish you keep in the tank.

If you’re quarantining Goldfish, or other cold water species, no need for a heater.  Conversely, tropical fish will require a heater.

I will say that I highly recommend using a heater that has a built-in guard. This will keep fish from accidentally brushing against the heating element and burning themselves.

Rocks and Decor

Again, don’t try to get fancy with plants, rocks and decor.

I do think it’s good to put a little something in there to give fish a place to hide. Fake plants are a good choice, especially plastic ones that you can bleach to sanitize them.

You mainly want something that is easy to remove when you need to do something in the tank or catch fish. And it’s best if it’s really easy to clean.

Transferring Fish

It’s best to have the tank set up a few days before transferring fish. Have the heater and at least some form of aeration to keep the water moving. 

Make sure that the temperature in the quarantine tank is stable.  

I prefer to drip acclimate fish in order to avoid rapid changes in temperature, GH, KH and/or pH.

Please, see our in-depth, step-by-step article about methods for acclimating fish, here. Mishandling shipped fish can cause major ammonia spikes, especially fish that have been in shipping bags for prolonged periods. Please, proceed with caution.

Once you have the fish acclimated and in the tank, you can go ahead and add the seasoned filter media. 

Clean Equipment

If you are concerned that new or sick fish are carrying harmful pathogens, make sure that no equipment, like nets or gravel vacuums, gets used in both display and quarantine tanks.

Keeping separate equipment for the different tanks will keep bacteria or viruses from hitchhiking from one tank into another.

If you can’t have separate equipment, you can sanitize some items with bleach. Please, see our article about sanitizing decorations, here. The same steps for bleaching hardscape items can be used for other kinds of equipment, like gravel vacuums and other plastic items.

How Long to Quarantine Fish

This is always a really tricky question. My best piece of advice: exercise patience.

Some diseases can take weeks to cause symptoms. Fish often mask being sick until their illness has become quite advanced. So, a fish might be sick for two weeks before you see any indication.

I would recommend quarantining new fish for 3 weeks to a month. 

And fish recovering from illness, I would recommend quarantining them for a full two weeks after they were last visibly sick. Many illnesses or parasitic infections can rebound, so it’s best to be cautious.

I know that these recommendations may seem extreme, but I’m a big believer in, “it’s better to be safe than sorry.” 

Final Thoughts

The biggest challenge to overcome when it comes to quarantining fish is making sure that the tank has a sufficient filter bed to be able to efficiently process fish waste.

Adding seasoned filter media from your existing tank is, in my opinion, the best way to combat this issue.

This will jumpstart the cycle in your quarantine tank by introducing large numbers of beneficial bacteria.

I highly recommend being very patient when quarantining fish. I know what it’s like to have new fish, that you’re eager to get into the display tank, but it’s better to wait and avoid introducing a disease or parasite to your established fish.

I hope you find this article helpful.

I wish you and your fish the very best!

Katherine Morgan
Katherine Morgan

Hey, there! I'm Katherine from Northwest Florida. An aquarium specialist, I've kept tanks for over two decades, enjoy experimenting with low-tech planted setups and an avid South American cichlid enthusiast.

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