Articles Water quality

How to clean an aquarium filter

August 2, 2016
cleaning aquarium filter

After setting up your aquarium and succesfully getting everything up and running, it can be easy to forget to do regular maintenance. Weekly water changes are something most aquarists will remember to do, but there’s more to keeping your aquarium healthy: don’t forget to pay some attention to your filter as well! It contains all the beneficial bacteria that allow your fish to survive.

This means filter cleaning is something that shouldn’t be taken lightly – keep reading for everything you need to know to keep your aquarium filter clean without damaging the bacteria colonies that make it so effective.


Note: if you’re not sure what the beneficial bacteria in your filter are or what they do, you might have missed a crucial part of setting up your aquarium, the cycling process. Find out what cycling your tank is and how to do it here.


When to clean your aquarium filter

When it’s time to clean your filter depends on a few different factors, such as how heavily your aquarium is stocked, how powerful the filter is and how much filter material it contains. A good indicator is the outflow: it seems to become less strong, the filter is likely getting clogged and it’s time to clean it. Just keep a close eye on it and after a while you should be able to predict when it’s time for a cleaning based on the last time maintenance was performed.

How to clean aquarium filter

The most important thing to keep in mind, as discussed in the intro, is that your filter material contains the beneficial bacteria that keep your aquarium stable. This means that anything filter-related should be done very gently to prevent swings in your water quality. It also means that you should never replace all of a filter’s cartridge at once in an attempt at “cleaning”, despite what many pet- and aquarium stores will try to tell you. In fact, you don’t have to change a cartridge at all unless it’s become so dirty it can’t be cleaned anymore. When that happens, just change half and the other half after a few weeks. You can use a generic filter sponge pad for this, such as this one.

It’s important to know that beneficial filter bacteria don’t like being shocked. This means it’s not the best idea to just take out your filter sponge and rinse it with cold tap water: the changes in temperature and water quality will cause a much larger bacteria die off than necessary. Instead, when it’s time to clean the filter, just take a bucket of aquarium water and use that for cleaning.

Now, onto the actual cleaning of the filter. Not all filters contain the same filter materials, so we’ll discuss all of them one by one. More information about what the different filter media types do can be found here.

Filter sponge and biological filter material

Filter sponge and biological filter material

  • Filter floss. Filter floss (also called filter wool, filter pads) is meant to trap small particles to prevent them from clogging the rest of the filter, which means it will usually be the most dirty. Filter floss is not meant to use for long periods of time and it’s the only filter material that should be discarded after a few uses (depending on how dirty it is). To clean filter floss, take it out of the filter and squeeze and roll it between your hands in the bucket of aquarium water to get all of that dirt out. If you find this is ineffective, it’s probably time to replace the filter floss.
  • Filter sponge. Filter sponge is usually layered after filter floss (or, if you have a smaller filter, it might be the only filter material in there). Unlike floss, you’re not meant to replace it regularly: it contains a lot of beneficial bacteria. You can clean it as you would clean any sponge, just give it a few good squeezes in the bucket of water until dirt stops coming out.
  • Biological filter material. Bio filter material is not meant to remove debris from the water, and instead only exists in your filter to provide more surface area for beneficial bacteria to latch onto. It contains most of your bacteria and you should handle it very gently! Unless it seems very dirty, just leave it alone. If you do need to clean it, just carefully swish it around in the bucket of tank water until the dirt is removed from the surface. Don’t use sponges or brushes to “deep clean” it.

And that’s it! After the filter material has been cleaned, you can scrub the rest of the filter to remove any algae that might have grown on it. Place the media back in the correct order and turn the filter back on as soon as possible to prevent beneficial bacteria die-off. If you feel like you might have damaged the bacteria population, you can try adding some bottled bacteria to prevent any issues.


If you have any more questions about cleaning your aquarium filter or want to share some of your own filter cleaning tips, don’t hesitate to leave a comment below. Happy fishkeeping!


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