How To Change Aquarium Filter Without Losing Bacteria

Do you worry about upsetting the biological balance in your aquarium when its time to change the filter media?
Many aquarists fear that changing the filter cartridge, sponge and other media will lead to a crash in water quality.

It rarely happens but when it does, it can cause an aquarium disaster.
But there’s good news! Once you understand how biological filtration works, you’ll never have to worry again!

Defining biological balance

Its important to understand the basic biological principles that are at work in our aquariums.
For our discussion

“Biological filtration” is the process by which microbes purify the aquarium water.

Few aquarists really understand what is happening in the unseen microscopic world that is the driving force in a healthy aquarium.
Bacteria operate the primary waste disposal system in the aquarium.
Some bacteria consume complex organics like uneaten fish food and solid fish waste. Other bacteria use inorganic substances, like ammonia and nitrate, as their energy source.

This array of microbes must be present in the aquarium for the tank to be “balanced” and healthy.
The aquatic bacteria form the living biological filtration system in every aquarium. But there’s more to it.
Imagine a 1000-gallon aquarium and a 10-gallon aquarium, each with a properly sized filtration system.
Each tank contains only one guppy.
Which aquarium will have a more potent biological filter capacity?
Neither! Both aquariums will have the same bio-filter capacity. How can this be?

Biological filtration 101

One of the most basic principles of nature is the balance of energy. Here’s an example that makes it easy to understand. An owl population depends on a steady supply of mice in order to survive. If the mouse population declines, less owls can survive. Nature balances itself out based on food (energy). It’s the same with the bacteria in our aquariums. Back to our guppy example. One guppy can only create a small amount of waste (food for the bacteria). It does not matter how large or small the aquarium is or how fancy the filtration system.

Biological filtration capacity is determined by the amount of aquatic life that is living in the aquarium. The aquatic life produces a certain level of waste that can support a certain level of bacteria.

The biological filter can never grow larger than the available food (fish wastes) that are present in the aquarium.

That’s why the biological filter “size” with one guppy is the same no matter what size tank the fish is living in.

Myths about biological filtration

There are many myths and half-truths about “biological filtration” on the internet, books and even at your local fish shop.

  • One of these is that the bacteria that eliminate ammonia and nitrite (nitrifying bacteria) live exclusively in your filter’s bio-filter compartment.

  • A similar myth is that the majority of the tank’s beneficial bacteria population live in the activated carbon, filter sponge, floss and other filter media.

This has lead many aquarists to fear that changing the aquarium filter will lead to a biological crash, because filter changes throw away all of the good bacteria.
Through years of scientific research and testing, we’ve learned that under normal aquarium conditions the beneficial bacteria population live just about everywhere in the aquarium.

This includes the gravel, aquarium glass, plastic plants, ornaments and in even in the water.
But what about on filter media inside the aquarium filter? Don’t bacteria live on filter sponges, activated carbon and other biological filter media?
The answer is Yes and No. Not the answer you expected, right?
We’ll explain why.

The truth about the biological filter

Aquarium research, using hundreds of freshwater and marine aquariums, revealed some shocking facts about the biological filter and filter media like filter sponges, filter cartridges and special bio-filter media.
Initially it was thought that nitrifying bacteria needed a special “safe haven” to survive and keep the aquarium free of ammonia and nitrite.
Filter manufactures designed a variety of filter cartridges, sponges, chambers and media to provide a “home” for the bacteria.

The logic follows that if you changed the cartridge, rinsed the sponge filter or disturbed the bio-media you’d cause the tank to crash. But under controlled laboratory conditions this never happened.
Aquatic biologists decided to take a look at various filter media under the microscope. Using a Scanning Electron Microscope (SEM) the scientists discovered that there were no more bacteria living in the filter media than in other parts of the aquarium.

That meant that in established, healthy aquariums it was perfectly safe to change out filter cartridges, activated carbon and even replace bio-media without any fear of a biological crash.
In fact, millions of aquarium hobbyists around the world change their filter media without incident.
If there were not true, we’d be losing fish every time we service our aquarium filters. It would be a nightmare!
But we also know that some aquarists have experienced a variety of water quality problems after changing their filter cartridges, sponge filters and activated carbon.

Since lab tests and practical experience indicate this should not be happening, why do some aquarium hobbyists experience a problem after changing the filter?

We’ll explain why and how to avoid water quality problems when changing your aquarium filter.

How changing your aquarium filter can upset the balance

As we’ve discussed, the beneficial bacteria essential for clean, clear aquarium water will take up residence just about anywhere in the aquarium.
The bacteria do float in the water but the majority tend to form colonies on solid surfaces.
You’ll find bacteria growing on the aquarium glass, gravel surfaces, plants and in the aquarium filter.
So why do some aquarists have problems with cloudy water and poor water quality after changing their filter media? There are several scenarios that can lead to sudden water quality issues.
We’ll take an in-depth at look at each one.

1. The new aquarist

The new aquarist is really excited about their brand new tank. The “young” aquarium is still developing a stable population of waste-consuming bacteria along with billions of other microscopic aquatic life that balance out the ecosystem.
As soon as a little algae appear on the gravel it creates panic. Dirt! Something must be wrong!
So, the water gets drained and the gravel rinsed. The same thing happens with the filter and cartridge, ornaments.

All of this washing, scrubbing and rebooting of the developing ecosystem stops the biological filter from becoming established. This behaviour perpetuates the unbalanced condition, inhibiting the formation of bacteria colonies that eliminate toxic ammonia and nitrite.
These toxins rise, resulting in fish loss.
The worried aquarist responds by scrubbing out the tank to get rid of “disease”, starting the process over again.

The solution to this situation is to take a mostly hands-off approach for the first four weeks of the break-in period.

Algae will grow, the gravel will get a little dirty and the aquarium water may even turn cloudy for a brief period.
This is normal! There is no need to change the filter cartridge every week. Let it get dirty during the first 30 days. This is when the biological system is forming a stable ecosystem.
Minimal disturbance during the initial start-up will go a long way to ensure a clean, healthy aquarium in the future.

2. The deep cleaner

Even experienced aquarists can sometimes disrupt their aquarium’s bacterial balance.
It typically happens when a well-established aquarium undergoes a deep, thorough cleaning involving a filter change, gravel siphoning and a large water change.
None of these maintenance activities are inherently risky. Many aquarists perform this combination every month.

But in some instances, this type of deep cleaning disturbs enough bacteria to cause water quality problems.
The nitrifying bacteria that take care of ammonia and nitrite usually colonize on the upper layer of gravel while sludge-eating bacteria live deeper in the gravel bed. Gravel siphoning is a great way to prevent the build-up of organic sludge in the lower layers. However, in some cases the complete disturbance of the gravel bed causes a temporary disruption of bacterial activity. The filter change-out removes another source of bacteria that would have taken over while the bacteria in the gravel recovered.

All of this deep cleaning usually kicks up a lot of debris, creating cloudy water.
A big water change dilutes the cloud but also dilutes the free-floating bacteria that could have helped re-establish the biological imbalance. Its’ a triple punch that knocks out the biological filter’s stability.
No one can predict when deep cleaning will cause this type of crash.

The best approach is to keep the aquarium gravel clean by making smaller, more frequent cleanings.

Siphoning the gravel also helps you keep up with water changes. Some aquarists choose to alternate their filter media changes with other clean-up activities like gravel siphoning, to minimize the chances of disturbing the bacteria.

3. The lazy aquarist

If we’re honest, all of us can admit that when life gets busy we tend to neglect our aquarium.
But the truly lazy aquarist completely ignores the aquarium until something really bad forces them to do something.
It’s usually the sound of a clogged filter struggling to pump water through a mass of sludgy foam pads and activated carbon.
Slimy filter media do not purify the water.

In fact, the decaying organic sludge releases algae-promoting nutrients, harmful hydrogen sulfide and put stress on the filter motor.
Chances are pretty good that the aquarium glass is covered with algae and the gravel is compacted with decaying debris.
The aquarium is typically in bad condition and already on the edge of biological collapse.
Changing the filter media disturbs what few bacteria are alive and tips the balance toward water quality problems.

As a final task, the lazy aquarist decides to scrape the glass, sending algae fragments into the water. Algae that gets sucked into the filter immediately begins to decay, further impacting water quality.
The obvious solution is to properly maintain the aquarium so it does not get into such poor condition.

If you must “renovate” a neglected tank it is best to make small improvements over time.

If the filter is malfunctioning it must be serviced. A properly running aquarium filter will increase aeration and purify the water more efficiently. Test the water for pH, ammonia and nitrite every week during the clean-up to eliminate any surprise water quality issues.
Old, dirty aquariums usually become very acidic, which can also inhibit the nitrifying bacteria. Make several small partial water changes rather than one large one to reduce major pH changes.

4. Mystery crashes

Sometimes an aquarium can undergo a biological crash for no apparent reason.
In most cases the aquarium is a fully stocked, thriving ecosystem with good water quality.
After a filter change the water becomes hazy and may have an earthy odor.
Despite decades of observations in homes, laboratories and public aquariums, no one really knows what triggers this type of random biological upset.
Hazy water is caused by a bacterial “explosion” in the aquarium water. Normally all the different types of bacteria are in a state of harmony. They’re invisibly cleaning and stabilizing the aquarium.
A cloudy haze forms when one type of bacterial population, normally a heterotroph (organic-eating), undergoes exponential growth.
The water becomes cloudy because there are millions of bacteria floating around in the aquarium water.
Two things can go wrong and lead to fish loss:

  • The bacteria cloud is not pathogenic

    This means the bacteria are not disease-causing. But they are alive and consume a lot of oxygen. It is common for dense bacteria clouds to literally “suck the oxygen” out of the aquarium water. Fish will gasp at the surface, trying to get oxygen. The fish aren’t sick, they’re suffocating.

  • The bacteria population suddenly dies back to normal levels

    The dead bacteria begin rotting which uses oxygen and drives up ammonia and nitrite levels. Even if the fish survive, they’ll be stressed by the poor water quality. Due to a weakened immune system, the fish can become sick weeks after the water has cleared and things look normal.

Since there is no way to predict when a random mystery crash will occur, the best plan is to keep close watch on your aquarium after changing filter media or performing any significant kind of maintenance.

Low oxygen conditions require extra aeration, often more than your aquarium filter can provide. Having an air pump and air diffuser on stand-by provides an inexpensive life-saving solution in times like this or if the aquarium filter malfunctions.


Bacteria power the biological filtration process that keeps our aquariums clean and healthy. Aquarists should not fear changing filtration media.
Consistent aquarium care eliminates many of the causes of biological crashes and water quality issues associated with filter maintenance.
Avoid waiting to service your aquarium filter until something goes wrong. Maintaining a biologically stable aquarium is not difficult but requires diligence and consistency.
Frequent, regularly scheduled filter changes ensure the filter is working at peak performance and reduces the chances of disturbing your tank’s biological balance.