Water Change + Clean Filter = Killed Beneficial Bacteria? (Maintenance Myth Busted) YouTube thumbnail

Water Change + Clean Filter = Killed Beneficial Bacteria? (Maintenance Myth Busted)

“Don’t ever do a water change and a filter cleaning at the same time or you’ll kill off the beneficial bacteria!” Sounds familiar? It’s a very common rule of thumb in the aquarium hobby. (Even we have given this advice before as part of beginner’s top 10 mistakes!) 

Of course, the fact still stands: Cleaning your filter will disturb and kill off some of your beneficial bacteria (even if you clean your filter the right way).

However, we have a question for you: If beneficial bacteria do not live in the water column, which they don’t (they live on all your tank surfaces and on your biomedia), then why would it matter if you did a water change at the same time as a filter cleaning? 

This rule of not doing a water change and a filter cleaning at the same time is both true and false. Why? It all depends on your individual maintenance practices and your tank’s maturity level

  • Thus, if you’re a beginner aquarist with an immature new tank, then it’s true: you can’t do a water change and a filter cleaning at the same time. 
  • In contrast, if you’re an advanced aquarist with a cycled and mature tank, then it’s false: you can do a water change and filter cleaning at the same time. 

In this article, we’ll set this “rule” straight once and for all. In addition, we’ll also recommend when you can add beneficial bacteria to your aquarium. 

Dear Beginner Aquarists

When we say “immature,” it is a tank that’s either currently going through the nitrogen cycle or recently completed the nitrogen cycle. So in these early stages, any loss of beneficial bacteria can be detrimental to your fish. 

Also, most beginner aquarists tend to overdo things. For example; beginners can easily overclean by wiping down all the equipment and décor, doing too many water changes, accidentally vacuuming substrate, etc. (No judgment; we’ve all been there!)

As a result, most of your beneficial bacteria are removed – harming your tank (and your fish). While there aren’t any bacteria in the water column itself, there are tons of them on your décor, substrate, glass, and any surface in your tank (yes, even on your equipment). 

Complementing that with a filter clean, well, that’s a recipe for disaster! So for this reason alone is why this general rule exists – it’s directed at a tank’s early stages and beginner aquarists. 

If you’d like to learn more about when to do a water change as well as how to do a water change, click on the respective links. 

Dear Advanced Aquarists 

Now, advanced aquarists, you may remember overdoing things in the beginning. But now we’ve gained some experience, we’ve got a water change schedule, know when to clean our filters, plus, our tanks have matured

Thus, we understand that it’s okay to do water changes and a filter clean at the same time. In fact, we can easily do 80% water changes on a weekly basis. And if it’s time for the filter to get cleaned on that same day, we have no problems! 

Water changes of any volume will not affect your beneficial bacteria – they simply remove the harmful nitrates and replenish the tank with clean, mineral-rich water. Here are more reasons why you should do water changes

On the other hand, when you do clean your filter, you will disturb your beneficial bacteria. However,  having a mature, established tank, will not have a detrimental effect on your tank and bacteria levels. How? 

There are so many bacteria in your tank that they’re going to quickly reproduce. And as a result, you’re not going to get any with any ammonia- or nitrite spikes.  

Always Stay On The Safe Side

Whether you’re a beginner- or advanced aquarist, for the sake of your fish, always stay on the safe side. What do we mean by this? 

Seachem Stability

Each time you clean your filter, dose the filter itself with Seachem Stability. This will help reproduce any of the bacteria we may have lost. This may not be necessary but we need to stay on the safe side (don’t let the level of your experience get the better of you).

We don’t know about you, but we’d rather have a good night’s sleep, knowing that all the ammonia being produced inside these tanks is getting taken care of. 

If, for example, you have a new tank setup and you just did a filter cleaning, then we absolutely recommend you dose some Seachem Stability inside the cleaned filter (or any other “bacteria in the bottle”). 

The loss of beneficial bacteria in a filter cleaning can be significant, especially if you’re not doing it the right way –knowing how to clean a filter (the right way) will go a long way. 

When to Add Beneficial Bacteria to an Aquarium? 

There are four other distinct situations you’d want to add beneficial bacteria to an aquarium – we’ve only covered one of them; during a filter cleaning. The situations are as follows: 

  1. During a brand-new tank cycle
  2. Adding new fish to a tank 
  3. During an ammonia spike
  4. During a filter cleaning or filter replacement 

Learn more about each situation in our when to add beneficial bacteria to an aquarium blog. 

When To Add Beneficial Bacteria To Aquarium YouTube thumbnail


Whether you’re a beginner or an advanced aquarist, you’ll always need to stay on the safe side – for the sake of your fish and the environment they live in. Remember, we want our fish to thrive and not just survive! 

The general rule applies more to beginners than to experienced aquarists, however, the tank’s maturity level and your maintenance schedule have an effect. 

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