How To Clean Aquarium Filter Without Killing Bacteria

Betta ebook-ban

Last Updated on 2023-05-24

A filter is an essential component in any safe aquarium, helping to keep the water clean of any contaminants that can harm fish. However, not all bacteria present in aquarium water are bad, and you want to ensure you don’t eliminate that bacteria when cleaning your filter. 

There are steps to follow when cleaning your filter to ensure all the bad bacteria get cleaned out and the good bacteria that your fish need stay in the water. If you happen to make a mistake cleaning your filter, there are ways you can add the right bacteria back in and prevent it from being removed again. 

What Are Good Bacteria In An Aquarium?

Good bacteria are bacteria that are able to help reduce and eliminate the bad bacteria that will naturally build up in the water. Good bacteria is generated in your aquarium through your filtration system, but it also builds on the gravel and cycles through the water. 

The important bacteria are nitrifying bacteria, which essentially eat up the bad bacteria and turn them into beneficial bacteria that keep the water quality suitable for aquatic life. Bad bacteria naturally occur in the tank due to fish waste, and it can make fish really sick if it’s not taken care of.  

Why Do You Need Bacteria In Your Tank?

Bacteria sounds like a dirty word, but in actuality, it can be a very good thing when it’s the right kind of bacteria. Ensuring that good bacteria can remain in your tank will ensure that your fish thrive and stay healthy. 

Good Bacteria Keeps Water Clean 

As mentioned, good bacteria are essential to make sure that bad bacteria cannot linger in the water. Since there’s nothing you can do to prevent bad bacteria from occurring, having that good bacteria helps take care of the problem for you. 

Good Bacteria Can Reduce How Often You Have To Clean The Tank

Since good bacteria break down a lot of the buildup in your aquarium, it makes it so you don’t have to clean as often. This doesn’t mean you don’t have to clean at all. You should still be monitoring your tank and its water quality, but you’ll likely find that you don’t have to clean as much. 

Good Bacteria Eliminates Harmful Ammonia 

When your fish excrete waste, it contains ammonia. Ammonia is very dangerous for your fish if it’s allowed to fester inside their water. Nitrifying bacteria contain ammonia and convert it into nitrites, which are then made into nitrates, which are good bacterium that isn’t harmful to your fish. 

Good Bacteria Cleans Up Debris 

Outside of bad bacteria, other contaminants can accumulate in a tank. This includes things like food fragments and dead plant matter. Until you have the chance to clean up any debris, good bacteria will ensure it doesn’t contaminate the water with bad bacteria. 

Pet shop aquarium

Good Bacteria Keeps Water Clear

Outside of maintaining water quality, good bacteria can help with water clarity as well. Not only can cloudy water be bad for your fish, but it doesn’t look very nice either. Cloudy water can be an indication that something unsavory is lurking in your aquarium. 

Good Bacteria Keeps Fish Happy And Healthy

Your biggest priority when keeping fish at home should be to keep them healthy and happy at all times. No one wants to live in a dirty home, and this includes your fish. Good bacteria help keep their water clean, clear, and free of accumulating waste and debris, meaning your fish can swim around happily in peace. 

This good bacteria and the overall nitrifying process that occurs with good bacteria keep damaging ammonia at bay. Where there is too much ammonia present in a tank, it can start to deteriorate some of the more sensitive areas of a fish, such as its fins and tails. It is not a very pleasant process for fish to deal with high amounts of ammonia.

How Changing Your Filter Leads To Loss Of Healthy Bacteria 

Your filter is responsible for creating and maintaining good bacteria in a tank. This bacteria is created through the cycling process and continues to flow from the media in the filter into the water. Depending on how you change your filter, you can end up removing all of these positive bacteria, which will allow the bad bacteria to thrive. 

Not changing your filter appropriately can very quickly take that healthy bacteria out of the water, leaving the bad bacteria free to roam around the water. This is what’s referred to as new tank syndrome. When changing your filter, be sure you’re doing so carefully to prevent new tank syndrome, which can shock your fish quite quickly. 

It’s important to follow the right steps when it comes to either changing your filter media, cleaning out your filter, or changing the entire filter system altogether. Neither of these filter maintenance steps are overly complicated, so taking that extra time to do things right is absolutely worth it. 

How To Change Your Aquarium Filter

There are a few methods you can use to change your aquarium filter. Some take less time than others, some require more work on your end, and some are less expensive options. The method you choose will likely depend on how much time you have and what seems easiest to you. 

Keep Your Old Filter In The Aquarium

When you’re looking to add a new filter to the aquarium, let the old filter remain in the tank. Keep it inside the tank until the new filter has time to build up new bacteria. The process takes about four to six weeks, but it’s one of the best ways to change your filter. 

Change The Filter But Keep The Old Media  

You can take the media within your old filtration system and put it in a new one, but this can only happen if the two filters are the same or are at least the same size. You can keep this old media in the new filter for about a month before it’ll need to be changed. 

This isn’t the most effective method to use, but it will ensure that good bacteria is kept in the water while bad bacteria are still eliminated. 

Place The Filter Cartridge In The Tank 

If you don’t want to keep the old filter in your tank in its entirety, you can take out the cartridge with the media inside and place it into your tank. Just be sure that both parts are in decent condition before placing them back in the tank. 

Set up your new filter, and keep both the cartridge and new filter in the tank for a few weeks so the new filter has a chance to build up good bacteria deposits. 

Don’t Change The Filter When Doing Other Maintenance 

You might be tempted to change the filter while you’re also doing a water change or maintaining your aquatic plants. It’s not recommended you do multiple types of maintenance at once so you don’t disrupt your fish for too long. Furthermore, you could be removing too many good bacteria at once, which is exactly what you’re trying to prevent. 

Only Change The Filter When Necessary 

You might feel the need to change the filter often in an effort to maintain water quality, but changing the filter too often can actually have the opposite effect. You’ll be able to tell when the filter needs to be replaced by monitoring the water quality by testing and viewing how the water flows in the tank. 

If you are changing the filter media, whether that’s sponges or another mechanism, and you’re not noticing much of a difference in water quality, this is a good sign that you need to replace the filter itself. 

betta care facebook group

How To Clean An Aquarium Filter Without Killing Good Bacteria

Aquarium filters need to be cleaned, but how you clean your filter is paramount to maintaining the presence of good bacteria in your aquarium. Depending on the filter you have, there are a few ways to clean the filter without killing good bacteria. 

Know What Filter Type You Have

There are multiple types of filters available for aquarium usage, and each will have its own particular recommendations for how to clean them. You should be sure to double-check the kind you purchase as you’re purchasing it. If you forget to do this and aren’t quite sure what you have, take a picture and show it to someone in an aquarium store or pet store. 

Replace One Sponge At A Time 

You should have at least two sponges in your filter. These get quite dirty over time and need to be replaced. Replacing one at a time ensures that all the good bacteria present aren’t going to get thrown out, putting your tank into shock. 

If you happen to only have one sponge, you can cut it in half and keep that in place, and add another sponge. Once it’s time to change sponges again, keep the full sponge in place and add another one. 

Clean Filters In Tank Water

Take some of the water from your tank and put it in a container, and use it to clean your filter. This will ensure that those positive nitrites that you need in your tank stay in the filter, but all the gunk and buildup get cleaned out. You never want to clean a filter with tap water, filtered water, or soap. 

Clean One Filter Element At A Time

This is only applicable if you have a three-stage filtering system, which is a great system to have. The namesake refers to three separate components within the filter that work together to keep the water clean. Cleaning one component at a time will ensure that good bacteria is never eliminated from the tank. 

Clean One Filter At A Time

Especially large aquariums may have more than one filter installed. Be sure you are only cleaning or changing one of these filters at a time. This will ensure that there is enough filtration still present in the aquarium to continue the nitrifying process. 

Don’t Clean The Filter Too Often 

You should only clean your filter every four to six weeks to ensure you’re not cleaning out the good bacteria. This is true regardless of the method you ultimately choose to clean your filter.

You might end up having to replace the filter media more often, but you don’t need to clean all components of your filter unless you notice it’s not working as effectively as it used to. 

Test Water Quality For Good Bacteria 

There are aquarium testing kits readily available that can help you monitor the presence of bacteria in your tank. Making an effort to test before and after you change or clean your filter can help you make sure everything goes according to plan. 

What Happens If You Lose All The Bacteria?

If you remove both good and bad bacteria from your aquarium, it will impact the water quality. As you know, the water quality of a tank is crucial in creating a suitable environment for fish, regardless of the type of fish you keep at home. If you take out the entire filter to replace it, you’re going to be taking the majority of bacteria out of your tank. 

While there will still be some present in your substrate or in other areas of the tank, it’s not nearly sufficient enough to maintain the integrity of the water. It’ll only take a few days or so before the amount of ammonia in the tank gets so high that your fish will suffer and will likely pass away shortly after. 

The good news is that you would have to intentionally clean the tank improperly in order to clear out all of the necessary bacteria. This is why educating yourself on aquariums and all their complexities should be done before you decide to purchase one. Each of the steps to take for replacing and cleaning filters is relatively easy to do, even if you’re a beginner. 

What Else Can Kill Good Bacteria In A Tank

Using improper techniques when cleaning a tank can kill good bacteria pretty quickly, jeopardizing the health of your fish. Be sure you are doing water changes slowly and appropriately, only taking out about 25% of the water at a time. You also need to ensure you use the right kind of water; generic tap water is highly discouraged due to its high chlorine and fluoride content. 

Additionally, when you are cleaning your tank, don’t try to deep clean every component of the tank at once. Split up your cleaning protocols so you’re not doing too much at once, disrupting and potentially shocking your fish. You don’t want to disrupt the oxygen cycle in the tank, as doing so can kill the good bacteria as well. 

There are other factors that contribute to the removal of good bacteria. For example, if your fish gets sick and you have to give them medicine, it could potentially alter bacteria. A lack of proper lighting can do this as well, so having a backup light if your power goes out or the light dies is important. 

Frequently Asked Questions 

Whether you’re building an aquarium for the first time or are just generally curious about how bacteria introduces itself into a tank, it’s good to know how the process works to ensure you have the right environment set up for your fish of choice. 

How Do You Get Good Bacteria In An Aquarium? 

When you first set up an aquarium, there’s a cycling process that must occur before introducing any fish. This is a long process, but it’s essential to build up that good bacteria in your tank.

Cycling will involve filling your tank with the right amount of water, adding in all the accessories, and running the filter, among other steps. It takes about four to six weeks to do properly. 

Good bacteria will essentially cling to other surfaces of your aquarium, ensuring that it stays in the tank throughout the various cleaning protocols you’ll have to implement to keep the aquarium suitable for your fish. There isn’t enough of the good bacteria that spread through the tank without the filter, so you can’t rely on this when cleaning or changing your filter. 


Maintaining a strong and efficient filtration system in an aquarium takes work. However, the work is worth it when it comes to keeping your fish healthy. Knowing how to properly clean a filter and how to change it can ensure you don’t remove the bacteria your fish need to function well. 

It may seem counterintuitive to want to keep your filter somewhat “dirty” with bacteria, but some level of bacteria-filled filtration is necessary in your aquarium at all times. Without the nitrifying process continuously occurring in your tank, you may lose some fish. As such, make cleaning and changing your filter properly one of your highest priorities, and your fish will thank you for it.

Ultimate Betta Fish Care Guide
About the author

Hey! I'm Nicolas from Iguane Media !

Blogger and Owner of the betta care fish guide
Thanks for reading this blog

I'm an Animal Lover