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How to Change Aquarium Filter Without Losing Beneficial Bacteria



How to Change Aquarium Filter Without Losing Beneficial Bacteria

Aquarium filters are crucial for maintaining the health and well-being of fish and other aquatic life. They work by removing debris and harmful substances from the water, creating a healthy and stable environment for your fish to thrive in. 

 However, changing aquarium filters can be a daunting task, as it often involves removing the old filter and replacing it with a new one.

This can disrupt the delicate balance of beneficial bacteria that have grown in the old filter, which are essential for maintaining the water quality in your tank.

In this article, we will explore how to change aquarium filters without losing the beneficial bacteria, ensuring a smooth transition for your aquatic pets. 

Why Do You Have To Preserve the Good Bacteria in Your Tank? 

Preserving the good bacteria in your aquarium is crucial for maintaining a healthy and safe environment for your aquatic pets. The nitrifying bacteria is a crucial component of your tank and without it the ecosystem of the aquarium will go haywire. 

These bacteria help to break down harmful toxins in the water, keeping it safe and healthy for your aquatic pets. Harmful toxins like ammonia is processed by the nitrifying bacteria and turned into safe substances.

These bacteria also help to maintain the clarity of the aquarium water. Without these bacteria, your aquarium can suffer from a buildup of harmful toxins that can cause your fish to become sick or even die. 

How to change aquarium filter without losing bacteria? 

Keeping the colony of beneficial bacteria in a filter is essential. Without the beneficial bacteria, the toxic substances will not be processed and it will harm your fishes in the end.

Therefore, you should not lose any of the bacteria while you are change your aquarium filter. It can be a daunting task as it can disrupt the balance of beneficial bacteria that have grown in the old filter, which are essential for maintaining water quality in your tank

Fortunately, there are ways to change your filter without losing these valuable bacteria. Here’s how: 

1. Consider a 3-stage filtering system

Having a filtration system that comes with 3 stage filtering is the most convenient for an aquarium.

It not only does its job efficiently but cleaning or changing the filter media is extremely easy as well and you will not lose the beneficial bacteria at all. 

The three-stage filtration system contains different kinds of filter media. 

  • Mechanical filtration contains pre-filter ceramic coils or rings. 
  • Chemical filtration has activated carbon as a component. 
  • Biological filtration has sponges with which its filters the aquarium. 

Not with three separate components, the beneficial bacteria have more space or area to populate. The nitrifying bacteria grows and accumulates in all three filter media, so cleaning and hanging them separately doesn’t get rid of good bacteria from your tank. 

But do not change them all at once. Do it gradually and make sure to remember the filter media that you have changed last. You will have to let the media function for about 6 weeks for the nitrifying to grow on it. 

Therefore, with a three-stage filtration system, the nitrifying bacteria have no chance of disappearing from your tank. Cleaning and changing are easier without the loss of any beneficial bacteria.

2. Always clean filter media in old tank water 

Regularly cleaning your aquarium filter is essential for maintaining a healthy and thriving aquatic environment for your fish. However, when it comes to cleaning the filter media, it’s important to use old tank water rather than tap water. 

It is a must that you preserve bacteria in your filter media. Beneficial bacteria form colonies in the filter media and therefore cleaning them in the old tank water is necessary.

If you do it in tap water, then the chlorine present in the tap water will wipe out all the beneficial bacteria. 

All the filter media need to be cleaned in the tank water. Get some tank water in a bowl or a bucket and get rid of any dirt and unwanted substances from the filter media in it.

Cleaning in old tank water will help you preserve the beneficial bacteria. These bacteria are essential for maintaining a healthy environment for your fish, so it’s important to preserve them during cleaning.

3. Run the Old Filter and New Filter Together Before Removing 

When it comes to changing your aquarium filter, it’s important to do it in a way that preserves the beneficial bacteria that have colonized the old filter media.

One effective method is to run the old and new filters together for some time before removing the old filter. 

The new filter that you install will not have any beneficial bacteria on it and therefore you will have to keep the old filter running along with it for some days.

With this, there will be no shortage of nitrifying bacteria in your tank. You will have to keep the old and new filter running for about 6 weeks and within this time the beneficial bacteria will make colonies in the new filter. 

But before doing this you must see the preferences of the fish species that you have. Two filters will increase the flow rate of the tank and this might be too much for some fish species.

4. Put the New Filter in an Empty Tank First 

Keeping and running the new filter in an empty tank before adding it to your main tank helps in preserving bacteria as well. You can do this if you cannot run two filters in the same tank.

But by running it in a new tank you can let the bacteria grow in the filter. Therefore when you add the new filter, it will not hamper the ecosystem of your tank. 

But simply running the new filter in an empty tank will bring about the beneficial bacteria. There are some steps you have to follow. They are: 

First off get your filter ready, add the filter media, and set it up. 

The next step is to set up the tank. Fill the tank with water and test the water for ammonia, nitrate, and pH levels. Note down the levels of the parameters. 

Then add ammonia to the water column. 

Set up the filter in your tank and let it run. 

Let the filter do its work for about three days. After three days, test the water for ammonia levels. If the ammonia level is lower than 2 ppm then you have to add some more ammonia. 

You have to follow these steps every day for 4 to 6 weeks. When 6 weeks have passed, the new filter will have enough bacteria to be in your main tank.

How To Know If Your Filter Change Reduced Bacteria? 

Filters are a vital part of maintaining a healthy and clean aquarium, and changing them is an essential aspect of aquarium maintenance.

However, changing the filter can also lead to a reduction in beneficial bacteria, which can harm the overall health of your aquarium. 

An obvious sign of a decrease in bacteria after a filter change is an ammonia or nitrite spike in your aquarium.

Beneficial bacteria are responsible for breaking down harmful waste products, such as ammonia and nitrite, into less harmful substances, so a decrease in bacteria can lead to an increase in these compounds. This can result in the death of fish and other aquatic creatures.

Another way to tell if your filter change has decreased bacteria is by observing the behavior of your fish. Fishes will tell you in a lot of ways that the beneficial bacteria have decreased in your tank.

If they appear lethargic or disinterested in food, it could be a sign that the water quality has decreased, and harmful toxins are present in the water. 

Also, the fish will begin to develop red gills, and bloody veins will appear on the fish’s skin. The worst thing is that the fish will die in your aquarium.

How Often Should Aquarium Filters Be Changed? 

Changin the filters comes in the process of maintaining a healthy aquarium. It is not necessary that you change your filter every 2 months or so.

You only need to change it when it get broken down or begins to run inefficiently and begins out dirty water

But make sure to preserve the beneficial bacteria in the filter. You can follow the steps mentioned above to preserve the filter media while changing aquarium filter. 

When it comes to filter cartridge changes, you should do it once a month. Filter media need to be changed when the water flow of the tank becomes slow. 

Change tank filter sponges one at a time 

Changing all the filter sponges at once can lead to a significant loss of good bacteria in your tank.

The filter sponge is the primary site for beneficial bacteria growth, which helps to break down harmful ammonia and nitrite compounds into less toxic nitrates that can be absorbed by aquatic plants.

The beneficial bacteria in the sponge are critical to the overall health of your aquarium ecosystem. 

When your filter has two sponges, then you should change one of them first. One of them should be kept in the filter because it will have a lot of beneficial bacteria within them.

Don’t change the other one for about 5 weeks, you will have to let the beneficial bacteria grow in the new filter media. After bacteria has found its way into the new sponge, then you can replace the other one with a new one.


In conclusion, changing the filter in your aquarium is an essential task that you should perform regularly to maintain a healthy aquatic environment for your fish and other aquatic life.

However, replacing the filter can also lead to a significant loss of beneficial bacteria in your tank, which can negatively impact your aquatic life’s health.

By following the tips outlined in this article, you can change your aquarium filter without losing beneficial bacteria and keep your aquatic life healthy and happy.

Remember to maintain a consistent schedule for filter maintenance and take proper care of your aquarium to ensure the best possible environment for your aquatic friends. 

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