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Cleaning Your Aquarium Filter: What You Need To Know

Cleaning Your Aquarium Filter: What You Need To Know 1

Let’s explore how to clean your aquarium filter. We will also go over all the different kinds that can be commonly found in the aquatic hobby. The purpose of your filter is to remove bad contaminants in the water column. Over time these bad particles get caught up in the filters media. You will need to clean this media in order for it to rid your tank of waste. I recommend that you set up a regular routine for cleaning your filter.

How often you should clean your filter depends on the type and also what kind of aquarium you have. If you have a heavily planted tank it may go longer without needing to be changed, since the plants will also act as a natural filter. If you keep messy aggressive type fish that will clog up the filter in no time, requiring more frequent attention.

Likewise, if you have a lot of fish, then that means they are producing a large amount of bio waste. You would want to clean the filter more frequently in this case. This way the filter can be at its prime in order to keep the water crystal clear.

There are basically three types of filtering processes happening in an aquarium filter:

Mechanical Filtering – Moves water through media to physically remove particles from the water column. This mechanical process could be from sand or a sponge catching particles as they are forced through.

Chemical Filtering – You would pick an active medium, most commonly Activated Carbon. Removed organic material that is not covered by other filter types.

Biological Filtering – Bacteria colonies will grow on the medium and break down organic particles as they pass through it.

Before I explain how to clean your filters, I need to go through a little bit about the different types. Not all of them will work the same way and will need different attention applied to them. I find the one thing that remains constant across all filters is the need to periodically clean them. A clean filter will keep your tank healthy, if it isn’t clean, then it cannot do anything for the tank. Fish can get stressed by not having optimal water conditions.


  • Hang on Back Filter – I would say that this would normally be the first filter that an aquarist will use. It comes with nearly every aquarium tank setup. It hangs on the back of the tank and down the backside. It has an inlet tube which pulls in the water and pushes it up through the filter medium hanging on the back and then waterfalls into the tank repeating the cycle. This medium can be as simple as a sponge or complex like bioceramics with lots of nooks-and-crannies to house bacteria. The splashing waterfall return can cause large amounts of water evaporation. I always keep an extra hang on back filter just in case my main filter dies, I can swap it out on the fly. These are among the cheapest option for filtering your aquarium water.
  • Sponge Filter – In this setup there is a power head that pulls large volumes of water through a sponge and right back into the tank. It is submerged within the tank itself. You attach a filter sponge to it. This is done for two reasons, one so that it blocks your fish from getting caught in the blades, the other is so that the water pushes through the sponge and gets filtered. This can be a quick temporary fix if you main filter goes down.
  • Powerhead Filter – I would describe this one as a combination of the sponge filter and the hang on back types. It uses a powerhead and sponge similar to the Sponge filter but also has a waterfall dispenser like the hang on back type. Definitely a cheap solution and gives you the ability to change out the powerhead when it goes bad.
  • Canister Filter – The canister filter is most likely the most efficient type of filtration and is the one that I use for all of my tanks. It provides excellent coverage of the three filtering types, mechanical, chemical, and biological. These filters are for larger tanks and are made to push large amounts of water volume. Similar to the hang on back, this filter has an intake tube pushing the water through the filter medium, then out. This time though the water goes through an output tube that dispenses below the water surface, not a waterfall like the hang on back. The canister itself is a sealed container, with several layers of a different medium which each serve different purposes.
  • Internal Filter – Being more of a specialized filter, this one is usually very small in size. You would usually see this in a nano tank where it is built to be as aesthetically pleasing as possible, while also taking up little space.
    Undergravel Filter – This is a system of panels that you would have to put down below your fish tanks substrate. Then it is connected with tubes to the surface. You run air pump lines down the tubes which creates movement. It creates a pocket of air that allows it to have water flow under the soil preventing stagnation.


Cleaning Your Aquarium Filter: What You Need To Know 2

Okay, for starters go ahead and power off the filter. I take a big Home Depot bucket and place my filter in there. I take this outside so I can clean it without dirtying up the house. You will want to work quickly enough so that the filter media doesn’t dry out, there is still good living bacteria there that we want to keep.

After getting inside the filter remove the medium. I take this under the hose and blow away as much of the large debris as possible. I then place it into some water so that I can clean the rest of the filter while this soaks. The medium can be different types, from ceramic rings to promote bacteria growth to activated carbon to kill off anything that passes by.

I proceed to clean the canister or container. I like a handheld dish scrubber that I got at the 99¢ store. This can be a cheap way to scrub the hard to clean slime algae from the inside of the filter.

You want to make sure you are getting around all of the seams and edges. In the case of a canister filter, the lid contains the pump. I make sure to get in this compartment using an old toothbrush.

Note: Make sure you do not lose any small pieces because the filter will not work without them.

I then use a bottle scrubber, also purchased at the dollar store, to clean inside the filter intake and output tubing. This could be somewhat difficult due to the length of the tube. Sometimes I have to put water in it and shake while plugging the ends. Let the debris to fall out, repeat until you no longer see waste particles coming out.

Now at this point, I will put the filter back together. Make sure you are inserting your media bags into the filter where they sit flush and do not have gaps on the sides. If there are gaps then the flow of water will go around it since it will be the least resistance. A filter with spaces in the media will not allow it to properly clean the water.

When I bring the filter back to the tank I fill it up to the top with water before powering it on. This allows the water level to be high enough for the pump to pull it and eliminates the air pockets. The pump needs water-tight pressure in order to be able to pull water from the tank and push it through the medium. Make sure that the lid is flush and secure to prevent water leaks.

Some pumps will have a primer handle that you pump up and down to remove the air bubbles. Others like the hang on back filter do not have this and are dependant on the water level being at the right height.

Note: Never run your aquarium filter dry, this will burn out the motor and in many cases ruing the filter itself. In most filters, you will be unable to change or repair the motor.


Cleaning Your Aquarium Filter: What You Need To Know 3

There are other filters that can be built at home. Do-it-yourself filters can be similar to a sand swimming pool filter. You pump the water from the tank to the bottom of the filter. The water pushes up through the sand and particles get removed. I wouldn’t call this the most efficient of filters since it doesn’t contain any chemical or biological cleaning, only the force of the mechanical type. This would probably be used for large projects like ponds.

One of my favorite filters are plants. Plants are often overlooked when considering filtration, but the reality is, plants are natures filters. They take in bad toxins such as ammonia, nitrates, and nitrites, then they give out oxygen as the byproduct. The fastest growing aquatic plants will really offset how hard the aquarium filter has to work. You can find plants as the only filtration method in low-tech Walstad aquascapes.

A UV Filter will be similar in shape to the interior filter but serves a different purpose. It will take in water into its dark, light-sealed chamber and it then shines UV light, killing algae and bacteria. This can really help clean up the water column making it crystal clear. While this can be useful, it is not meant to fully replace the aquarium filter only augment it.

Surface Skimmers will filter the water surface only. This helps in removing the oily film that can build up on the surface. Provides for optimal CO2 and Oxygen exchange. The aquarium light will be able to penetrate the surface better as well. If you want a spotless water surface then you want to use a surface skimmer. Like the UV Filter, this is not meant to be a full tank filtering solution.

You can also create your own sponge filter with an air pump and some tubing. This works similar to the under-gravel filters explained above. You get a sponge filter without the motor, then put the air tube down the sponge filter tube. The rising air will cause the water flow to go through the sponge and out the tube.

Of course, if you are tired of filter cleaning there is an alternative, the Water Garden Aquarium. This is a unique setup, usually in nano size. It has a platform that plants grow into and their roots feed on nutrients in the water column. They get the nutrients from the fish itself. You only need to provide fresh water through weekly water changes. The other alternative is a low-tech Walstad tank which doesn’t require a filter either.


Determining how often to clean your filter will be different for each setup. You do not want to do too frequent of changes since this could kill off beneficial bacteria and in turn, hurt your fish.

Sometimes you need to do frequently almost back-to-back filter cleanings if there is something really wrong in your tank. Maybe you have a spike in nitrates or ammonia, which can be caused by a buildup of biowaste matter in the filter. You may need to do another cleaning after waiting a bit just so you get all of it.

If you have a breeding tank where there isn’t a substrate, then you will have to clean your filter more often. The waste doesn’t have anywhere to settle so that it can get removed by your fish, shrimp, or snails. This excess will ultimately get sucked up into your filter and requires a more sudden cleaning.

If you are using sponge filters you will need to clean the sponge every couple of weeks. With my canister filter,s I can go several months before needing to clean it. I have even had one tank go 6 months before I had to take action. I wouldn’t recommend this though since it can be very risky for your fish. You do not want to stress your fish by not keeping a clean filter.

Check out this video from Everyday Aquarist on YouTube, you can get a good understanding about what it takes to clean your filter from this video. It is a Fluval filter but you can get most of what you need to know from it for any of the canister filters. Some of the same principles apply for any filter though.


Cleaning your aquarium filter is one of the most important ways to maintain a healthy aquarium. The filter is the main thing that keeps the aquarium ecosystem going.

When cleaning your filter media make sure you are not letting dry out. You want to keep it moist so that we can maintain the beneficial bacteria that reside in it. If you kill off the bacteria in the filter then it can create a situation similar to new tank syndrome. This would effectively make you have to cycle your tank again. This can be very stressful on the fish.

I always recommend having an extra filter on hand in case yours dies suddenly. This has happened to me before, it was a holiday weekend where I wasn’t able to get another one as easily. You do not need to keep a second fancy filter though, a cheap hang on the back filter can serve this purpose just fine.

I hope you have found this article useful. When first getting into aquarium keeping understanding all of the different filter types can be confusing. They can all serve the same purpose but in different ways.

Now go clean your aquarium filter!

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