How to Clean Aquarium Filter Sponge: Guide & Tools to Use

how to clean aquarium filter sponge
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Freshwater shrimp, injured fish, and slow-water fish all require clean water without overpowering water currents. While filter sponges aren’t the most efficient, they serve a vital purpose in some situations.

That’s why… 

Knowing how to clean an aquarium filter sponge is a skill that may come in handy as you gain experience with specialized aquarium care situations.


Over time, I’ve definitely moved further away from high capacity filtration and towards the “less is better” camp.

This comes from a wealth of experience with observing fish and other aquatic creatures interact with each other and the environment around them.

Even though we can’t always see the water currents in the fish tank, the creatures that live in the tank are very aware of them.

Sadly, high-capacity filters can do a lot of harm because they can generate currents that are too fast for the creatures in the tank. 

This can lead to darting and panicking, which increases the risk of injury. Depending on the fish species, excess water current can also disrupt gill function.

While I’m still not the biggest fan of sponge filters, I have moved more in their direction and tend to use them more than I did years ago.

Knowing how to clean an aquarium filter sponge is very important. Unlike other mechanical filter media where you can let things slide, a sponge filter will clog very quickly and become useless.

Impact of Cleaning on the Biofilter

Set of bio balls for fish tanks

In most aquarium filter systems, the floss or sponge media is where beneficial bacteria are most inclined to colonize.

Unlike other filter types, you don’t always have the luxury of staggering media changes so that the biofilter recovers faster.

Therefore, when compared to other filter types, it is very easy to do more damage or completely destroy the biofilter when you clean a sponge filter.

Limiting Impact of Cleaning on Biofilter Housed in the Filter Sponge

There are 3 ways to limit damage to the biofilter each time you clean the sponges:

  • Use a minimum of 2 sponge internal filter units for every 3 gallons of water in the tank. This will provide plenty of filtration and make it easier to stagger cleanings. 

Your goal is to go 3 to 4 weeks between cleanings and then only clean one filter sponge at a time. This ensures other sponges in the tank are fully colonized with beneficial bacteria. 

  • Only clean the filter in cycled aquarium water.

    This ensures the water doesn’t have any chemicals or contaminants that might kill off the beneficial bacteria.

  • Never completely clean the sponge. An aquarium filter sponge isn’t like the sponge you use to do dishes. In that instance, removing soap and other debris from inside the sponge is essential. 

When it comes to an aquarium filter sponge, this kind of harsh cleaning is also likely to dislodge beneficial bacteria. 

Your best bet is to gently remove any external algae or sludge buildup. From there, just squeeze gently on the sponge once or twice.

The Best Water for Cleaning an Aquarium Filter Sponge

Most people recommend using old tank water directly from the aquarium and using it to clean the filter sponge. I don’t like doing it this way because you will wind up having to put more water back in the tank.

In general, once your tank is well balanced, I don’t recommend using a routine water change schedule.

Instead, you should only have to top off the water from time to time to manage evaporation. Keep an eye on the hardness and pH, but don’t make changes unless you have to.

Anything else can disrupt the pH or other water parameters beyond what you would want.

To clean a filter sponge properly, you will need at least 1 gallon per sponge.

Now bear in mind that gravel and other objects tend to reduce the amount of water actually sitting in the tank. 

As a result, a 10-gallon tank may actually only have 8 gallons in it. If you take out 1 gallon, you will be removing more than 10% of the water. This is enough to wreak havoc for fish that are especially sensitive to water quality changes.

Your better option is to keep a separate, fully cycled tank water on reserve for cleaning filter sponges. You can keep aquatic plants in there as well as have them ready for emergency needs. 

While removing water from this tank will still have an impact, at least it won’t be upsetting your community tank.

Additional Tools for Cleaning the Aquarium Filter Sponge

Filter Sponge for aquariumOther than aged aquarium water, the most important tool is a clean bucket for cleaning an aquarium filter sponge.

Unlike many other filters types on the market, you will have to put your hands in the water to remove and install the sponge filter.

Your hands and arms must be clean before you put them in the tank water.

This includes making sure your hands don’t have any traces of soap, skin moisturizers, or other contaminants on them. 

I prefer to use an aquarium-safe hand cleaner and a hand/fingernail brush so that my hands are as clean as possible before I put them in the tank. 

When you are done working in the tank, you can use any kind of sanitizer and soaps to wash your hands and arms. 

I also recommend keeping a separate hand/fingernail brush for post-tank scrubbing so that you don’t wind up contaminating the tank water the next time you have to work in it.

You may also want to invest in some powder-free, aquarium-safe gloves. These will protect your hands from all the gunk on the filter. 

 If you decide to get into saltwater reef tanks, you will also find it very useful to be in the habit of putting gloves on first.

When to Replace the Filter Sponge

Once aquarium filter sponges clog up, it is very hard to save them. This is why cleaning them often and preventing debris from working its way inward is so important. 

If you take good care of the filter sponge and keep the bioload on the light side, you can get several months out of a filter sponge.

You will still have to replace the sponge when you notice reduced bubbles are coming from the sponge even after you clean it. 

While you can get away with upping the airflow to the airstone for a short period of time, the filter will still have internal clogs. This, in turn, will create reduced efficiency. 

This short video is a good example of that: 

Fun Fact: Another important facet of aquarium maintenance is knowing the frequency of filter medium replacement. Learn more on how often to change aquarium filter to maximize your filtering system’s performance!

Frequently Asked Questions

1. Is there a way to get chemical filtration with a sponge filter?

There isn’t a way to add activated carbon, zeolites, or other chemical-based filter media to a filter sponge unit. 

Instead, you may need to put nylon stockings filled with these kinds of media around the tank. Since sponge filters generate very little water current, you will also need to add airstones to the socks.

This filtration may not be as robust as in other filters, but it may still be enough to keep the tank clean.

2. Should I soak the sponge overnight?

There is no need to soak the sponge overnight when cleaning it. 

All you will do is run the risk of the sponge sitting in water that might not be in the ideal range for preserving the biofilter housed within the media.

3. Why shouldn’t I clean an aquarium filter sponge in tap water?

There are three main problems with using tap water to clean an aquarium filter sponge. First, tap water contains all kinds of chemicals aimed at killing bacteria. Chances are, the good bacteria in the sponge will be killed off.

Second, it is all too easy to make the water too hot or too cold. If you go outside of the optimal temperature range, it will kill off the good bacteria.

Third, as strange as it may sound, you may wind up over-cleaning the sponge. Remember, the goal is to remove debris and gunk. You don’t want to flush out all the good bacteria housed inside the sponge pores.


Learning how to clean an aquarium filter sponge will give you an important tool as your understanding of aquarium care evolves.

Once you get away from the idea that robust water currents are the best way to keep a healthy tank, you will develop a strong appreciation for how useful sponge filters can be.

Last Updated: July 11, 2022

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