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How to Clean an Aquarium Filter: 6 Expert Tips

Lindsey Stanton Profile Picture

By Lindsey Stanton


Aquarium filters do an excellent job of keeping your aquarium water clean; likewise, they need to be cleaned after a certain amount of use. If a filter is left uncleaned for long periods, it may release the dirty water back into the tank. The filter motor will burn out if left clogged, leading to a hazardous electrical and heating situation.

Therefore, a filter must be cleaned on a regular schedule, and we hope to break down the basics of filter easy and cleaning for you, with an in-depth method for ensuring your aquarium filter is kept clean in minimal time.

aquarium plant divider

Types of filters

There are two prominent types of filters: internal and external.

  • Internal filter: sponge, under gravel, slide-in box media, or cartridge filters
  • External filter: hang-on-back, canister, or Fluval filters
How to determine when you should clean your aquarium filter
  • The flow is slower
  • The motor is becoming hot
  • Visible gunk and debris near the intake
  • The water is getting visibly dirty (cloudy, floating particles)
  • Water parameters (ammonia, nitrite, nitrates) spike
Benefits to cleaning your aquariums filter
  • Prolongs the lifespan and durability of the filter
  • Cleans the water more effectively in a shorter period
  • Preventing the filter from overheating

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To successfully clean your aquarium filter, you need to make sure you have the materials and method.

  • Prepare a bucket of old tank water. It is best NOT use tap water as this will kill off the beneficial bacteria.
  • To make cleaning your filter easier, you have the option of purchasing aquarium cleaning brushes instead of using an old toothbrush or your hands
  • Turn the filter off and unplug it. Be cautious not to wet the plugs or outlet.
  • Lay down a towel to catch any water spillage.
  • Keep an aquarium net on hand to catch debris that will release from the filter once it is off.
  • Note: Keep all the components of the filter submerged in a bucket of tank water. If the beneficial bacteria are in the air for a short period, they will start to die.
Image Credit: Igor Chus, Shutterstock
How to clean an internal filter
  • Step 1. Begin by removing the internal filter from the water. Use a net to catch any of the debris that flows out into the water when you lift it.
  • Step 2. Place the filter into the bucket of old tank water, let it sit for 30 seconds while you gently swish it around under the water to loosen debris.
  • Step 3. Start to disassemble the filter components into the water, make sure each part stays submerged.
  • Step 4. Use an aquarium brush or old toothbrush to scrub the visible gunk off the sponge. You may have to do this repeatedly.
  • Step 5. If the tubing or impeller is clogged, use a thin aquarium brush or earbud to dislodge the gunk and clean in between the blades.
  • Step 6. Lastly, rinse the components in the bucket of old tank water and begin to reassemble the filter. The filter should be clean and ready to be placed back into your aquarium!
Image Credit: Igor Chus, Shutterstock
How to clean an external filter
  • Step 1. Begin by turning off and removing the filter from the outside of the tank. Unplug the cord and make sure it is kept dry.
  • Step 2. Remove the inside of the filter component that needs cleaning. Do not submerge the whole filter unless stated safe by the manufacturer.
  • Step 3. Place the filter media or canister media container in a bucket of old tank water. Let the filter media soak for 30 seconds. Then begin to swish the media around in the water to free any dirt particles.
  • Step 4. Start to use an aquarium brush or an old toothbrush to clean the gunk from the filter intake and output. Then clean any small spaces with a small impeller brush or earbud.
  • Step 5. Scrub any debris off the filter media and impeller and then dunk the media into the bucket repeatedly.
  • Step 6. Reassemble the filter components and place the media back into the holder. You can take this opportunity to replace any old filter media that may be losing its value.  It is best to make sure the parts are all in place before you turn on your filter. You have now successfully cleaned your external filter!

Reducing the need for frequent filter cleaning

Cleaning a filter can be tedious and undesirable. Luckily, there are ways to reduce the need to clean your aquarium filter.

  • Avoid overfeeding your aquarium inhabitants, as excess food gets sucked up by the filter’s intake.
  • Stock your aquarium appropriately. Keep the waste in the aquarium at a minimum, thus preventing your filter from being clogged with excess excrement.
  • Use a filter that filtrates twice the amount of water volume than the aquarium holds.
  • Gravel vacuum your aquarium’s substrate more frequently to pick up loose debris.
  • Do not skimp on water changes. Remove any excess debris in the water.

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Alongside filter cleaning, you do not want to clog your filter up too frequently. Over time, this damages the motor leading to your filter having a shorter working span or making it less effective. Check the manufacturer’s website to ensure you are taking apart the correct components without damaging a part of the filter. Cleaning filters can be tricky. We hope this filter cleaning tutorial has helped you to maintain and keep your filter from getting clogged.

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Featured Image Credit: Andrey Nikitin, Shutterstock

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