How to clean an aquarium filter




cleaning aquarium filter

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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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6 thoughts on “How to clean an aquarium filter”

  1. I have 2 fancy goldfish one is a blackmoor and the other is a cyclic. The water has been cloudy for 2 weeks now. I have a spong filter and a double marina internal filters so white cloudy water. I have not bothered to clean them out, just that I used filter start only a couple of droplets a week ago and have gravel. Established tank. Plant food so my filters are now really clogging. My goldfish are fine however why should I leave them in their own poo and wee? Doing partial water changes once a week. How does this work in the real world. It stinks of poo. No ammonia just a fishy odour. No heater now as it seems too warm. No drafts not near a window UV light, not closed glass aquarium with hood, large square on a cabinet. They are both 3 years old. What is in cloudy white water? Is it ok to leave them to get so filthy? I am yet to understand why I have always done the right thing by cleaning them out with fresh water which is delchorinated in buckets clean buckets left to room temperature and how you clean a clogged filter in dirt ridden filthy water actually is correct or do you only buy baby goldfish and what lifespan do they have?

    • Hi Georgina,

      I’m having a little difficulty understanding your setup, but as long as you have 0 ppm ammonia and 0 ppm nitrite with all other good parameters, I wouldn’t worry too much. There are many reasons why your tank might be cloudy: bacteria bloom, excess sunlight, waste. But in these cases, I’ve found it’s better to let your tank jumpstart itself than to interfere as long as water parameters are safe.
      Also, yes. Fish tanks do have quite a unique smell to them!

    • Hi Bella,
      This mostly depends on your aquarium setup as you will need to decide how strong of a filter, how much space for media you actually need, as well as how much space you can designate for your filter from inside the tank. In general, it’s best to always go with as big as you can with filters, though internal ones can take up a lot of space and that’s definitely something to consider.
      Many hobbyists like Eheim, Fluval, Marineland, or even Aqueon products.


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