How to Clean a Fish Tank (Without Killing Your Fish)

cleaning fish tank
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Every time my mother cleaned the fish tank, I knew our goldfishes were going to die within a day or so.


Back then, I didn’t know anything about biofilters, fish slime, or fish stress.

When it comes to learning how to clean a fish tank, you have to take into account how that activity impacts the creatures that live in the tank and the water chemistry.


Water is water… right?

When it comes to your aquarium, the answer is no. As fish and other aquatic creatures live in the tank water, they also change the chemistry.

Things like hardness, pH, and nitrogen levels are just a few things that change as fish and other creatures carry out basic metabolic activities.

If your tank is cycled properly, these changes happen gradually, over days, weeks, and even months. During that time, the animals and plants in the tank will also adapt.

Unfortunately, when you clean the tank or do a water change, the water chemistry changes suddenly. If the change is too much, it can lead to ruptured swim bladders and a whole host of other internal problems.

Each time you clean your fish tank, you should know how each activity will affect the following:

  • Damage to beneficial bacteria – can range from minimal up to 100%.
  • Sudden changes in water chemistry and their impact on fish physiology.
  • Damage to the fish’s slime coat and the increased risk of illness.
  • Fish stress and its relationship to injuries.

Water Testing and Its Role in Partial Water Changes

fish tank water pump

In general, the best way to clean a fish tank is to avoid it as often as possible.

Water testing can help you eliminate unnecessary and damaging partial water changes.

If the water chemistry is within range for the creatures in your tank, just top off the water if it needs it. Don’t forget to add the water conditioner, especially if you are using tap water.

From there, just keep an eye on fish behavior until the next scheduled testing. Once you get accustomed to changes in fish behavior, you will come to rely on that more than testing to see if you need to clean the tank.

Setting up an Aquarium Cleaning Schedule

Top-to-bottom cleaning in one session is the fastest way to wreak havoc on every aspect of the ecosystem in the tank.

You are much better off addressing aquarium cleaning with a schedule that looks something like this:

  • Weekly – Test for ammonia, nitrates, nitrites. Add zeolites and nitrogen pillows if needed.
  • Weekly – Test hardness and pH before and after topping off. Adjust as needed.
  • Monthly – Week 1 – 4 if the substrate is dirty – vacuum ¼ of the aquarium gravel each week. 
  • When vacuuming gravel, use partitions and a temporary corner filter to suck up free-floating debris.
  • A motorized gravel vacuum will also distress the fish-less because you don’t have to deal with priming the siphon manually.
  • Monthly – change the activated carbon in the filter. 
  • Monthly – clean algae with an algae scraper if needed and trim live plants.
  • Monthly – Check on the floss to make sure it isn’t rotted. Replace any rotted filter media.
  • Bi-monthly – Rinse 50% of the floss in cool water to eliminate debris.

Time of Day Matters When Cleaning the Tank

Depending on the species of fish in your tank, some may be more active in the day, while others are more active at night.

Let’s say you have a tank dedicated to goldfish or some other fish that is most active during the day. If you clean the tank in the morning up through noon, the fish will be skittish until the tank is finally dark enough for the fish to fall asleep

By contrast, if you clean the tank closer to dusk, the fish will only be stressed for a few hours. When fish are stressed for a shorter period of time, there is a much better chance of them being calmer the next day.

The reverse is true if you have nocturnal species of catfish or others in the tank. In this case, you will be better off cleaning the tank in the morning.

If you have both types of fish in the tank, then choose cleaning time based on the activity and the fish most impacted.

For example, bottom-dwelling fish are usually nocturnal. If you have to clean the gravel, install a temporary partition and clean during the day hours.

If you have to do a partial water change on the same tank, do that during the early evening hours when diurnal fish, which live in the mid to upper regions are getting ready to go to sleep.

Why You Shouldn’t Clean Right After Feeding

feeding in aquarium large dry food

In a natural setting, fish compete for food. Even if you provide enough food, stress levels among tank mates will still go up when food is present.

Normally, this stress isn’t enough to cause the fish to vomit.

Nevertheless, the fish’s overall stress level is still elevated. Therefore, if you go to clean the tank, the fish is already starting off at an elevated risk state.

Contrary to popular belief, fish can and will vomit if they are stressed out.

At the very least, wait 2 – 3 hours after feeding before you do any cleaning in the tank. This gives the fish a chance to digest and calm down after eating.

How to Clean a Fish Tank Using Temporary Partitions

Reducing fish stress while cleaning the tank is essential. One of the best ways to do that is to install a temporary partition.

This will keep the fish away from the gravel cleaner and any other device you may use while cleaning the tank.

Let’s say you have neon or glass tetras in the tank. These fish are notorious for darting when they are stressed. That includes right under a stream of fish tank gravel as it leaves your gravel siphon.

The best way to prevent them from getting hit by falling debris is to make sure they can’t swim into it, to begin with.

When you clean the gravel, a huge cloud of fish waste and rotted food will be released into the water. Without a partition to block it, the waste will quickly spread all over the tank.

Depending on the filtration rate, it can take anywhere from an hour to several hours for the water to clear up again.

A partition will shorten that time considerably because there is less spread in the debris field. I also recommend installing a bubble filter with floss in the blocked-off area of the tank.

The temporary filter will pull in the waste quickly, thus avoiding adding blunt debris to the main filter. If you use HOB filters or others that are inclined to clog, this is the best way to reduce the risk of that problem after a gravel cleaning.

Never Use Soap or Detergents When Cleaning a Fish Tank

Soaps, detergents, and glass cleaners can all be toxic to fish and other creatures in the tank. No matter how slimy a toy may be, or covered in algae…

You should only use water and an algae pad to clean them off.

If you must use some kind of cleanser, only use ones that are made specifically for the type of aquarium you are keeping. In some cases, cleansers for saltwater tanks are not safe for freshwater and vice versa. 

Why You Should Avoid Using an Algae Scraper

When you use an algae scraper, some of the algae will dissipate into the water. Since algae need light to grow, it will die when it gets trapped in a filter or in other areas with no light.

This, in turn, can lead to a deadly ammonia surge.

I recommend avoiding algae scrapers as much as possible. You are better off keeping algae eater fish or other creatures like snails and shrimp in the tank.

Even if you have just one betta fish in a small tank, adding a snail or shrimp reduces or eliminates algae without creating tankmate issues.

And here are more tips on how to clean fish tanks for a beginner:

Fun Fact: Cleaning a big aquarium when you are still a beginner is quite daunting! We suggest starting with a decent 20-gallon fish tank to acclimate yourself with lesser stress and challenge.

Frequently Asked Questions

Do you take the fish out of the tank when cleaning?

Unless the fish is dead, there is never a need to remove fish from the tank during cleaning.

When cleaning the tank, there should never be a need to remove all the water.  There is no need to remove the fish during a partial water change.

In the rare situation where you need to do a 100% water change, be sure to move the fish to another tank with sufficient water, filtration, and room to live.

If the fish tend to be skittish, simply partition them off until you are done with the water change. Usually, what fish can’t see won’t bother them.

The partition will also help absorb some of the increased water currents as water is added to the tank. 

Should you clean fish tank gravel?

A lot depends on how the gravel looks and what kind of creatures you have in the tank.

As long as there is no tank debris sitting on top of the gravel, there is no need to clean it.

Seeing some debris mixed into the gravel is ok if you have plenty of live plants and scavengers.

The debris will break down and become food for the plants. Some scavengers also rely on the debris for their food.

If you have artificial or plastic plants and no scavengers in the tank, then you may need to clean the gravel from time to time.

What is the best way to clean your tank?

The best way to clean a fish tank is in stages and over time. Gradual changes reduce the risk of fish stress and dangerous fluctuations in the water chemistry. 


Cleaning a fish tank without killing the fish is mostly about optimizing when you do the cleaning. There are also some very simple tools like temporary partitions and filters that will make the job much easier and less stressful on the fish.

I hope this article answers a lot of your queries and helps you in taking good care of your finned friends!

Last Updated: July 6, 2022

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