Hepper is reader-supported. When you buy via links on our site, we may earn an affiliate commission at no cost to you. Learn more.

How to Clean a Fish Tank After Disease: 6 Tips & FAQs

Lindsey Stanton Profile Picture

By Lindsey Stanton


Disease can ravage a fish tank and its population, and in a very short period of time at that. We are not here to talk about the different diseases, though. We are also here today assuming that you have already cured your fish of their diseases. However, what we are here to talk about today is how to clean a fish tank after disease.

If you do not do an excellent job at cleaning the tank after any kind of disease, it might just come back to finish off your fish. Whether viral, bacterial, or fungal, you need to take the proper steps after the disease is gone in order to ensure that the fish do not get sick all over again. Let’s talk about how to clean a fish tank after disease right now.

aquarium plant divider


The 6 Steps to Take to Clean a Fish Tank After Disease

To make things as easy on you as humanly possible, we are going to go through a simple step-by-step process on how you need to clean your fish tank after disease. Let’s get right to it!

1. Remove Fish

Remove all of the fish from the tank and put them in a temporary quarantine tank. It’s not really a quarantine tank as much as it is a place to put the fish while you clean the tank.

empty fish tank with net and decorations
Image: Alexander Geiger, Shutterstock

2. Remove Everything Else (Including Substrate)

Remove everything that can be removed from the tank. This means taking out plants, decorations, rocks, caves, driftwood, and anything else of the sort. You will also want to remove filters, lights, pumps, and all of that other fun stuff too.

Once you have removed everything, you should be left with the substrate in the tank. Some people say that vacuuming the substrate is enough, but in our opinion, it’s not. Bacteria and other infectious agents can linger in sand and gravel, so the best bet is simply to replace it altogether.

At any rate, remove the substrate and throw it in the trash. You can use a cleansing solution for the substrate if you like, but in our opinion, it is better to just change it altogether.

3. Use a Cleaning Solution

Mix a cleaning solution that is roughly 10 parts water and 1 part bleach. You want to take an algae scrubbing pad and use the solution to clean the interior and exterior glass walls of the aquarium.

Make sure to properly rinse the aquarium out after doing so because your fish definitely will not appreciate bleach being present. The bleach helps to kill viruses and bacteria, but you do need to make sure that you wash out all remnants of the bleach once you are done cleaning.

aquarium cleaning
Image Credit: hedgehog94, Shutterstock

4. Clean Your Filter

Take your filter and clean it. If the disease was really bad, you might actually want to replace the media. Yes, this does mean getting rid of all mechanical, biological, and chemical media. One problem you will face here is that you will remove all beneficial bacteria from the water, which is bacteria that your fish need to stay alive.

However, after disease, you should be replacing all of the water anyway, which means that you will have to cycle the tank either way. At any rate, you want to use the bleach solution to clean as many filter components as you can, once again remembering to flush it all out thoroughly to get rid of any remaining bleach.

5. External Lights, Plants, Decorations, and Rocks

Wipe down any external lights and other such items with the same bleach solution. Just be careful that you do not damage any of the electrical components when doing so.

Rinse off and scrub down all plants, decorations, rocks, and other things in the tank with this same bleach solution. Once again, be careful to rinse everything thoroughly because you definitely do not want any bleach in the tank once you put your fish back in it.scrubbing clean aquarium decorations shell

Image: Sergiy Akhundov, Shutterstock

6. Put Everything Back in the Tank

Once you are satisfied that all of the components that could have even maybe come into contact with disease are clean and disease-free, you can start putting everything back into the tank.

On the topic of cycling, since you have changed the substrate, the water, and the filter media, you will need to go through the nitrogen cycle before putting the fish into the tank. If you do not want to spend weeks doing the cycling, you can always buy the beneficial bacteria in a bottle and add it to the water for instant cycling.

You might want to add some kind of fish medicine into the water in order to prevent the disease from coming back. As long as you know what kind of disease your fish had, using the treatment after the disease is gone as a preventative measure will help get rid of any remaining remnants of the disease and prevent it from coming back.

aquarium plant divider


Preventing Disease From Coming Back

There are a few things that you can do once you have cleaned the tank after the disease to prevent your fish from getting sick again. Follow these tips in order to engage in maximal preventative measures.

  • Never add new fish straight into an existing tank habitat. You always want to quarantine new fish to ensure that they show no signs of disease. If they do show signs of disease, make sure to get rid of the disease before adding the fish into the tank. If the fish shows no signs of disease after 2 or 3 weeks, you can add it to the tank.
  • Try to feed your fish only good-quality fish food. Your fish need the proper nutrients in order to have a strong immune system in order to fend off disease. At the same time, make sure that any live foods come from good places. If the live foods are infected with disease, chances are that they will be passed on to your fish.
  • Make sure that you provide a suitable habitat for your fish. A well-functioning filter can go a really long way in removing disease from an aquarium. At the same time, cleaner water means that your fish will be healthier and have a stronger immune system, thus enabling them to fight off disease with maximum efficiency.
  • Always make sure to clean filters, do regular water changes, and clean the tank at least once per week. Like we said, cleaning the tank and removing threats from the tank before they manifest in disease is always good.
  • Never transfer things from one tank to another. This goes as far as the nets you use for the tanks. This can easily cause disease to spread from one tank to another.

aquarium plant divider



How Do You Disinfect a Fish Tank After a Fish Dies?

Fish can leave disease behind and bacteria can develop, especially if a dead fish is left in the water for any prolonged period of time.

First off, you should remove the other fish from the tank and place them in a separate tank. To be safe, remove all water from the tank and start with new water, making sure it has been dechlorinated.

You will want to let the tank go through a nitrogen cycle before adding new fish. Remember that while filter media can be cleaned, when a fish dies, the recommendation is to replace all filter media, if possible. Also, you will want to wash the plants and the substrate in hot water to disinfect them. Anything that can be boiled should be boiled, and the rest needs to be cleaned and scrubbed thoroughly.

cleaning aquarium
Image Credit: Sergiy Akhundov, Shutterstock

Can You Bleach Fish Tanks?

Yes, in extreme cases, if you are worried about diseases and bacteria sticking around, you can use some bleach to disinfect a fish tank.

You should use roughly 1 part bleach and 19 parts water to rinse out your fish tank. Be sure to follow this up with a thorough rinsing in warm water until you can no longer smell the bleach, then rinse for another couple of minutes, even after you can no longer smell the bleach.

Remember that bleach is very poisonous, and if there are any remnants of it leftover in the fish tank, it can very well spell disaster for the entire tank.

aquarium plant divider



The bottom line is that you need to take every precaution possible in order to prevent diseases from coming back to wreak a second round of havoc on your fish. It is up to you to keep your fish healthy, safe, and disease-free.

Featured Image Credit: MARVIK, Shutterstock

Related Articles

Further Reading

Vet Articles

Latest Vet Answers

The latest veterinarians' answers to questions from our database