How to Change Aquarium Filter Without Losing Bacteria (Tips)

how to change aquarium filter
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Last Updated: July 11, 2022 by Flora Gibbins

When I started my first tank, I found myself desperately wishing I could just go buy some “aged water” to put in my aquarium.

Well, that’s because…

At the time, I thought that only meant the slime and other deposits that build up and make the water better for the fish.

I didn’t realize that learning how to change an aquarium filter without losing bacteria was a key element to getting that highly coveted old tank water.


Have you ever wondered how good bacteria get into a newly cycled tank, to begin with?

Even though you can’t see them, there are billions of bacteria in the air around you. Many of these bacteria use ammonia and nitrites for food.

Over time, these bacteria reach the water and begin the process of breaking down any ammonia or nitrite they come across.

Relatively speaking, taking a month or so to colonize aquarium water isn’t a long time.

Once you start adding aquarium fish, even a 24-hour reduction in nitrifying bacteria activity can spell disaster.

Since the filter is a key place for good bacteria to colonize, knowing how to change the aquarium filter without losing bacteria is essential.

Pros and Cons of Bacteria Additives

Waiting for a tank to cycle the first time can be difficult, especially if you are anxious to bring home some new aquatic pets.

Many people purchase bacteria additives in hopes that the tank will reach zero ammonia and nitrites faster.  Before you use these additives, it’s very important to understand what they can and can’t do.


  • You start off with an optimized set of bacteria instead of whatever happens to be in the air.
  • No wait time for the bacteria to reach the water.


  • Bacteria additives won’t propagate any faster than naturally obtained species.
  • If there isn’t enough food in the tank, the bacteria will still grow slowly or die out.
  • They aren’t anymore resistant to medications or toxins than local species. 

DIY Tricks to Make Small Hob Filters Friendlier to Good Bacteria

using gravel for good bacteria

Arthritis, sprained wrists, and cuts on your fingers are just a few things that make it hard to take care of an aquarium filter. In these situations, you may find you have to rely on a HOB filter for your tank.

While larger HOB filters have separate media cartridges, smaller ones usually have just a single cartridge. When you change that one cartridge, you throw out almost all the healthy bacteria that colonized the filter.

Since all water in the tank passes through the filter, this is a significant loss to the ecosystem in the aquarium.

The best way to prevent this from happening is to find a way to keep some of the old filter media in the aquarium.

Here are some ways to accomplish that:

  • Put extra floss in a nylon stocking and set it into the filter. Make sure you wait at least 3 weeks between changing or rinsing the floss and changing the main filter cartridge.
  • You can also use gravel or anything else that is highly porous in the stocking. Just be sure to use media that won’t dissolve in water.

Many people also make their own media for HOB filters. This includes creating custom mixes of zeolites, carbon, floss, and resins. You can even use sponges from the dollar store.

Aside from saving money, these DIY options have the advantage of being easy to change in stages. This, in turn, ensures there is always some colonized media in the filter.

Why You Need a Good Bacteria Bank

At first glance, you may not think it necessary to keep a spare biofilter on hand.

Each time you put your hands in the tank or add new creatures, there is a chance they will carry disease into the tank.

The only way to get rid of that disease will be to use antibiotics that are also likely to destroy the biofilter.

Aside from that, paint fumes, smoke, air sprays, and many other pollutants can get into the water and make aquatic creatures very sick.

If activated carbon doesn’t remove the toxin quickly enough, you may have to do a complete water change along with adding new filter media.

Under these circumstances, having a few gallons of water ready with active bacteria will go a long way towards getting your tank’s biofilter back up to speed.

This is distinctly different from bacteria additives that may have to come out of dormancy and then go through a process before they get up to speed. 

How to Set Up a Good Bacteria Bank

Once your main tank is up and running, you will need to set up a smaller second tank where you can keep good bacteria safe.

Make sure the tank has a tight-fitting lid. Keep it in a location where it won’t come into contact with any kind of fumes that might get into the water.

Put some gravel in the bottom of the tank, and then a small pump-driven filter. It does not need to have activated carbon in it.

Use filter floss or other material that has a lot of pores for the bacteria to colonize.

Fill the tank about 50% with water from the established aquarium, and the rest with clean water.  Make sure you also add a water conditioner for the new water.

From there, all you need to do is drop some food in from time to time. You may also want to keep live plants and some snails in the tank to keep it ticking over.

When you need to use the bank, take out half the water and half the floss. You can also take out some gravel to reseed the main tank.

bottles of water for aquarium

Filter Management While Medicating the Tank

Parasitic and bacterial infections are some of the worst things that can happen to your aquatic pets. They also spell disaster for the existing biofilter.

Once your aquatic pets show signs of disease, there is no way to save the biofilter. All you can do is restart it after treating the infection.

Depending on the infection, you may need to use two or three different medications followed by yet another medication to address secondary infections.

Before you add the antibiotic, add new media to the filter. Do not add activated carbon or anything else that might remove the medication.

Always discard filter media from contaminated tanks. Even though the media may still be housing beneficial bacteria, it is also housing the bad germs that require the medication.

No matter whether you only needed to use one medication or several, chances are the good bacteria in the gravel and other parts of the tank will also be killed off.

Restarting the Biofilter After Treatment

After treatment is over, you will need to filter with activated carbon for 2 – 3 days to make sure all the medication is gone.

Once this process is complete, you will need to scrub as much of the internal filter as you can with hot water to disinfect it. This will also help remove more residue from the medicine.

Depending on the filter type, you may not be able to get into every area.

Just do your best with what you can reach and get into.

After you clean the filter, insert new media. This is also the time to insert new floss from the good bacteria bank.

Upgrading Your Filter and Jump Starting Good Bacteria

If all goes well, there is a chance that some of your aquatic pets will live well over 20 years. By contrast, you may need to replace pumps and other moving parts of the filter system a bit sooner.

No matter whether you need to install a sponge filter or upgrade to a canister filter, the process of preserving the biofilter is the same.

All you need to do is take as much material from the old filter as you can and insert it into the new one.

If you have to wait a day or so before installing the old media, let it sit or float in the fish tank. Just make sure the media doesn’t dry out.

You can use a nylon stocking to cover the media to keep nosy fish from getting into it.

Fun Fact #1: If you have a big aquarium, then choose a bigger filter for better results! For instance, your 60-gallon tank could benefit from a 55-gallon aquarium filter to take care of water and bacteria.

Fun Fact #2: Your good bacteria could also benefit by having your fish tank cleaned on a regular basis. Learn how to clean a fish tank without killing your fish and grow healthy fish and bacteria!

Frequently Asked Questions

How to change an aquarium filter cartridge without losing bacteria?

The easiest way to do this is never to replace all the filter media at one time.

If you have a system with only one cartridge, find a way to place something else in the filter that will act as a preserver for good bacteria.

How will I know if I have beneficial bacteria in my aquarium?

During the process of setting up a new tank, you should test daily for ammonia, nitrites, and nitrates.

Even if you only have water in the tank and some bits of food, you will see ammonia coming up in just a few days.

You will know bacteria that consume ammonia are active and working when the ammonia levels go down to zero.

As ammonia levels come down, you will start to see nitrites go up. This means the bacteria that consumed the ammonia are now producing nitrites.

Next, you will see the nitrites go down, and nitrates come up. At this stage, the second type of bacteria that consume nitrites are active in the tank.

Even though you can’t see the bacteria, the changes in tank water chemistry tell you biological filtration is ongoing.

Later on, when you add live plants and fish to the tank, the lack of ammonia and nitrites is a reliable indicator that beneficial bacteria are present and thriving.

This video shows how to test aquarium water for pH, ammonia, nitrite, and nitrate:

How often should you use bacteria supplements in an aquarium?

If the aquarium ecosystem is healthy and balanced, you should never need to use bacteria supplements. 


Mechanical filtration and chemical filtration are important parts of keeping aquarium water clean and in good condition. Beneficial bacteria that colonize the filter and other parts of the tank are also very important.

Knowing how to clean the filter without killing off good bacteria is essential if you plan to take care of fish or other aquatic creatures successfully.

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