How to clean an aquarium filter

How To Clean Your Aquarium Filter Without Losing Good Bacteria

The majority of fish keepers will have a weekly schedule of maintenance that they perform on their aquariums. In most cases, this will include water changes, gravel vacuuming, and wiping down of the glass.

However, there’s another crucial part of your setup that you should be cleaning on a regular basis. This is your filter; the heart of good bacteria in your aquarium.

How often you clean your filter will vary dependent on several factors. These include:

  • How stocked your aquarium is
  • How powerful your filter is
  • How much filter material your filter contains

A good indicator that your filter needs cleaning would be the outflow. If this appears clogged and water flowing out of it has slowed, it’s probably time to clean it, and here’s how.

How To Clean Your Aquarium Filter

Before you start to clean your filter, it is important to remember three things. These are:

1. Your filter material contains beneficial bacteria that keeps your aquarium water stable. This means that any filter-related cleaning should be done carefully to avoid damage to your water quality.

2. You should never replace all of a filters cartridge at once as this will remove the majority of good bacteria. Rather, change ½ during one clean and ½ during another a few weeks later.

3. Never shock your media, it really doesn’t like it! By shock, we mean killing off beneficial bacteria due to using either very hot or cold water to clean it. Rather, you should use a bucket full of aquarium water, which no doubt you will be removing anyway during a water change, and use that.

Moving on to cleaning the filter it needs to be noted that not all of them are created equal. They do not all contain the same materials, so for that reason, we will look at them all.

Filter pads, Wool and Floss

Filter pads trap the small particles of dirt from your aquarium and stop them from clogging the rest of the filter. This is usually clearly the dirtiest part and will need to be changed on a fairly regular basis. They usually last for a few cleans, dependent on how dirty they get, before they will need to be replaced.

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To clean pads simply take them out of your filter and place them in your bucket of aquarium water. Once there squeeze them and roll them between your hands to remove all dirt. If you notice this isn’t working, it’s probably time to replace them.

Filter Sponges

Containing lots of good bacteria the filter sponge is usually found after the layer of filter pads. You should clean this as you would any other sponge by giving it a good few squeezes. This should be done again in your bucket of aquarium water and repeated until dirt stops leaking out.

Please note, some smaller filters only have a sponge for filter media, and that the sponge should never be replaced. This is due to it containing a good amount of beneficial bacteria that it would be harmful to lose.

Biological Filter Media

The biological media found in your filter is not meant to clean or remove debris from your water. Rather, it only exists to give your filter more surface area for good bacteria to grow. It is the place where most beneficial bacteria will be found and for this reason, needs very careful cleaning.

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Unless biological media is really dirty, you should leave it well alone. However, if you need to clean it, handle it very gently and never deep clean. Rather, you should carefully swish it around in aquarium water until all surface dirt is removed. Do NOT use brushes or sponges to clean biological media.

Finishing Touches

Once all your media is clean, you can now turn your attention to the housing of the filter. Scrub this to remove any dirt or algae that has grown on it before placing filter materials back in. When putting filter materials back in your filter be sure to get them in the correct order.

Finally, you will need to get your filter back up and running as quickly as you can. This will ensure that no good bacteria die off due to being out of your aquarium water for too long.

But What Is Good Bacteria And How Does It Help Your Fish?

You may, or may not, now be wondering what beneficial bacteria is and why it’s so important to your fish? Well, good bacteria is a key part of maintaining water quality, which as we know is essential for healthy fish.

There are two types of beneficial bacteria, the Nitrosomonas species, and the Nitrobacter, both of which are crucial to the nitrogen cycle. This is the cycle that we perform to break down all kinds of waste including:

  • Fish excrement
  • Uneaten food
  • Dead/decaying plants
  • Dead fish

As waste material decays it produces ammonia which is highly toxic to fish. Even small amounts of ammonia present in an aquarium can result in:

  • Damaged fins
  • Lethargy
  • Inflamed gills
  • Algae blooms
  • Swollen eyes
  • Possible death

Beneficial bacteria (Nitrosomonas and Nitrobacter) break down the ammonia in an aquarium into nitrites. This is the first stage of a nitrogen cycle which goes as follows:

Ammonia  → Nitrite  → Nitrate

Nitrites are still highly toxic to your aquarium fish but are dealt with and broken down by other bacteria. From nitrites come nitrates, as shown above, which are still slightly toxic but will not affect your fish in small amounts. Furthermore, other parts of your filtration will then help remove nitrates to keep your water quality at an appropriate level.

For a complete Guide to aquarium filters read our review of the Best filters for smaller aquariums or Best filters for larger aquariums.

Conclusion: How to clean an aquarium filter

As we have seen cleaning your filter in the right way is highly important, in fact, crucial to maintaining a healthy aquarium. This is because the good bacteria needed to start the whole nitrogen cycle is contained within it.

Clean your filter incorrectly and your aquarium will crash bringing catastrophe to your aquarium. But clean it right, as we have shown you, and you will have a happy aquarium filled with healthy thriving fish.

If you need any more help with your aquarium then read our Complete Guide To Starting A New Aquarium packed with all the information you’ll need to run a happy and healthy fish tank.

About the Author

Joanne Burn

Joanne has been keeping fish for many years both freshwater and saltwater and has been writing for fish keeping websites and magazines for even longer. Her fishkeeping knowledge, research and writing skill makes her an essential member of the fishkeeping forever team.