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Where to Keep Your Fish While you are Cleaning the Aquarium

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Every once in a while I do my regular maintenance for all my aquariums, and I recall asking my local fish store where I should keep my aquarium fish in the meantime. This is what he told me.

Where should you keep your aquarium fish while you are cleaning their tank? Simple, always keep your fish in the aquarium. Do not remove them from the tank during cleaning. Doing maintenance like cleaning the glass, vacuuming the gravel and trimming plants is less stressful than moving the fish. Furthermore, you should never remove all the water from the aquarium at once.

In the rest of the article I will explain to you why you can just leave the fish in the aquarium during cleaning. Also, I will give you a reliable regular maintenance scheme that you can use for your aquarium. This way of cleaning your tank will give your fish a safe place to live and will make sure you only do the necessary cleaning and nothing that is too much effort.

Why you should never remove all the water from the aquarium at once

When cleaning the tank, the main thing that you need to do is changing a part of the water. However, you should never change 100% of the aquarium water because it will actually hurt your fish.

Beneficial bacteria

Removing all the water can kill all the beneficial bacteria that are housed in your aquarium (especially in your filter). These bacteria break down the waste in your aquarium like fish poop, decaying food and plants. They transform ammonia (highly toxic) to nitrite (still toxic) to nitrate, which is less toxic.

If you were unaware of these bacteria, you should know they make up the ‘nitrogen cycle’ in your aquarium. This is also the reason why you should wait around 6 weeks before adding fish to a new aquarium. I have written an article a while ago that explains the cycle in more detail.

When you would change 100% of the water, there is no ammonia in the new water at all. This essentially is the food for the beneficial bacteria, and as there is none they will die. Yes, the fish will produce new ammonia, but depending on how many fish the new ammonia might come too late.

Adapting to water parameters

The other reason why you should not remove 100% of the water in your aquarium is because you will never get the water parameters like temperature, pH and GH to exactly match the original aquarium water.

Therefore it is best to only change a smaller part of the water and mix the remaining water with new water. This way, the parameter change will not be as drastic and therefore your fish will experience less stress.

As a small sidenote, it is always a good idea to know the ins and outs of aquarium water parameters. There are several ways to measure the parameters in your aquarium, and I have an article on this site that explains the meaning and the optimal parameters in our freshwater aquariums.

What is the best regular aquarium maintenance routine

Now that you know that you should not remove all the water from your tank, what is the right way to go?

If your aquarium is already cycled and settled, you should only have to do regular maintenance. While a lot of aquarium owners do things different (different frequencies, different amounts) I will share with you a reliable way that works.

Before I spill the tea I would like to give a quick disclaimer: if you have extremely messy fish like oscars or other so called ‘monster fish’ you will have to do more maintenance. Due to their diet and messy table manners there will be more waste floating in the aquarium.

Water Changes

Alright, so a good way to go is doing weekly water changes. And instead of changing 100% of the water, only change 25% of the water. This will make sure your nitrate levels remain low and you will not fall victim to nitrate values slowly building up over a period of weeks.

When you do not do your maintenance properly and only top off your aquarium instead of removing and replacing parts of the water, your nitrate levels will start building up to lethal levels.
This is called old tank syndrome, if you want to know whether your aquarium might have old tank syndrome, read this article I wrote.

Another thing you need to be aware of is treating your tap water before adding it to your aquarium. This is because the water directly from the tap is not safe for your fish as it contains chlorine and chloramine. Read this short article I wrote about dechlorinating tap water to make it safe for your fish and plants.

Finally, when adding the water back to your aquarium, make sure that you match the temperature as good as you can. You want the water you add to be the same temperature as the water currently in the aquarium to minimize stress to your fish caused by a difference in water parameters.

Gravel vacuuming

While removing the water from your aquarium, you should remove all the fish poop, uneaten food and dead plant matter from the bottom of the tank. While stores sell dedicated ‘cleaner fish’, this is by no means a replacement for doing maintenance.

So you are the one responsible for removing all the waste from the bottom. And luckily there are rather cheap tools to help you with this. The best one I have found for the price is this gravel vacuum on Amazon. This is a definite must for all fish keepers.

Filter maintenance

Next to doing water changes, removing waste from the bottom, cleaning the glass and pruning aquarium plants you must not forget to clean your filter. When you have a good filter, a lot of the waste will be removed from the aquarium, but it will still be in the filter. Out of sight is out of mind, but not out of the aquarium.

Therefore, once a month, clean your filter. Now to clean your filter, do not take out the filter medium to rinse it under the tap. This is a no-go as rinsing the sponges under the tap will kill/remove all the beneficial bacteria housed in your filter. And there are a lot of them, which you all need to take the bioload from your fish.

Instead of the tap, take a bucket and fill it with some aquarium water. Now clean the filter medium in the bucket by squeezing and shaking it around in the tank water for a while. Do not clean it too much, just make sure the big waste is out of it.

I am going to write it one last time in bold and underline, as I think it is that important and so many people kill their fish doing this: Never completely clean your filter by rinsing it under the tap and making it look like new!


Whenever you are cleaning your aquarium, do not remove your fish from the tank. Instead, leave them in. The cleaning will cause them less stress than being moved back and forth.

Also, never remove 100% of the water when cleaning your aquarium. Instead, replace 25% of the aquarium water with fresh water once a week.