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How Do I Clean My Aquarium? Part 2: Cleaning the Filter.

Making sure your aquarium filters are properly maintained ensures lower nutrient levels, optimal flow, and the removal of detritus in your fish tank. Replacing physical and chemical media removes organic matter from the water column and prevents it from decaying and breaking down into nitrogen and phosphorus based organic compounds that cause algae growth and toxicity at elevated levels.

Optimal flow is responsible for ensuring enough water passes through the filter so it can function efficiently. Flow is also responsible for proper oxygenation, preventing dead spots, and creating a natural environment for your fish, coral, and invertebrates. At peak efficiency, a properly maintained filter is most effective at running the full volume of water through your tank several times an hour, exposing as much water as possible to the filter media.

In this article, I’ll discuss three popular filter types and how to properly maintain them. The first is the hang-on-back (HOB) filter. This filter type is mostly used on smaller freshwater tanks, but can be used for virtually any system. It is inexpensive and easy to use, but does not allow much room for customization.

The second is the canister filter. This filter type is mostly used on small to larger freshwater tanks, but can also be used on saltwater aquariums. They cost a little more, but are easy to install and maintain. They also provide a little more room for customizing your filter media based on your tank’s needs.

The third type of filter I’ll discuss is called a sump. Sumps can be used for any medium to larger tanks of any kind, and are very common in saltwater setups. On smaller tanks, a sump-like filter is sometimes fitted into the back, inside of the tank. This setup is called an all-in-one and functions very similarly to a sump filter. Sumps are the most expensive filter option, but are prized for their nearly endless customizability.

Choosing the right filter will depend on your tank’s needs. Heavy bioloads should be fitted with sumps or canister filters. Smaller tanks with only a few fish, or beginner aquariums will do fine with a HOB filter. The more self-sustaining and autonomous you want your aquarium to be, the more you should consider a sump.

Hang-on-back Filter

Hang-on-back (HOB) filters have a compact design. They can house physical, biological, and chemical filtration. These filters are designed to straddle one of the four panes of glass of your aquarium. The intake tube rests inside your fish tank and the impeller pulls water from the tank into the impeller compartment then the main compartment. Once in the main compartment, water flows through the physical and chemical media, then the biological filter media, if present, before flowing out of the filter, over a lip that rests on the glass pane, and back into the tank.


HOB filters should undergo light maintenance once a week where you clean or replace the physical and chemical media as necessary. They should also be more thoroughly cleaned once a month.

Weekly Maintenance

Once a week, you can pull the physical media from the filter and inspect it for saturation and integrity. I define saturation as the level of detritus that has built up on the media. At the very least, rinse the media in dechlorinated water. You may have to rinse it out several times to desaturate it and return it to normal. I define integrity as the level of deterioration of the media itself. After several weeks of rinsing and scrubbing, the media floss begins to degrade and the whole physical media pad must be thrown out and replaced.

In some cases, activated carbon is sealed in the filter pad. If your tank has a relatively heavy bioload (a lot of livestock), the carbon should be replaced every 2-4 weeks. However, if it is sealed in the pad, and the pad is perfectly fine, you may want to add a secondary source of chemical filtration in a mesh filter bag if it fits in the filter’s main compartment. If the physical filter media is shot, but the carbon is still active, and sealed in the pad, you’ll have to throw the whole thing away anyway, or cut open the pad and remove the carbon. If the pad is old enough to be degraded, the carbon is likely spent as well.

Chemical filtration in the form of granular ferric oxide, carbon, zeolite, or mixed resin media should be replaced on a schedule recommended by the manufacturer. An aquarium with a heavy bioload needs chemical filtration replaced more often. Every tank is different. The best way to determine how often to replace your chemical media is to test the water parameters you are trying to remove with your specific media type. Test the water parameters (1) right after you add new media, (2) after one week, (3) and after two weeks, then compare those values. Based on how high the last two values are will determine if you need to replace once weekly, or twice or four times monthly. Nutrient limits are different for freshwater and saltwater tanks.

Biological filtration should never be replaced or washed. If your biological filtration becomes clogged to the point where it is no longer effective, rinse half of it in old aquarium water one week, and the other half a week later. Always make sure fully seeded biological filtration is present in your aquarium at all times.

Monthly Maintenance

Once a month, or every couple months for low bioload tanks, the entire filter should be unplugged, removed from the tank, and scrubbed out. This procedure is aimed to accomplish a couple things. First, you want to clean the impeller of debris. This prevents the magnet from scratching, and the impeller blades from clogging. Second, depending on the flow rate of your filter, detritus and debris will probably settle in the bottom of your filter compartments where they will break down into algae causing organic nutrients.

On most HOB filters, the impeller housing can be cleaned by first removing the intake tube from the impeller compartment. The impeller will either come out as well, attached to the intake tube, or it will remain in the impeller compartment, held there by the magnet. Either way, once the impeller is removed, rinse out the compartment with dechlorinated water and use a bottle brush to scrub out the inside of the magnetic housing where the impeller sits. Rinse off and replace the impeller and intake tube.

A basic sponge or scotch pad that has not been infused with any kind of cleaning product or soap can be used to scrub out the inside of the main filter compartment. Be sure to keep your biological filter media wet in old aquarium water while your cleaning your filter.

If there is an excess of hard water stains caked on the filter, a one part white distilled vinegar, three parts water solution sprayed on and scrubbed will remove most of it.

Once your filter has been reassembled and placed back on the tank, fill the main and impeller compartments with aquarium water until water begins to spill over the lip and back into the tank. Then, plug the filter back in as you continue to pour water into the main compartment until the filter is primed and begins to run water back into the tank on its own.

If you hear rattling, buzzing, or the filter is not priming, check the impeller to make sure it is both securely fitted into the magnetic housing and the intake tube.

Canister Filter

Canister filters are designed to fit neatly beneath your aquarium with two hoses leading up to the tank. One hose is the intake, the other is the return. With most canister filters, the hoses are connected by a quick release mechanism which allows you to lock the valves closed and quickly remove the hoses without removing the lid or leaking water from the hoses.

Most Canister filters incorporate baskets in their design. Each basket houses a different media type. Physical, chemical, and biological filtration easily fit within a canister filter, and can be modified according to your aquarium’s filtration requirements.


Due to the design of the canister filter, a thorough cleaning is just as easy as a light cleaning and should be done weekly. In order to do any maintenance at all, the filter must be unplugged, and opened up. Since you’ve gone to all that trouble anyway, you might as well make sure all parts of the filter have been cleaned.

Begin by unplugging the canister filter. Then, lift the lever that closes the quick release valve. This mechanism is usually located in between or adjacent to where the hoses are attached to the canister filter. Once the valve is closed, disconnect the hoses. Keep a towel ready as a small amount of residual water below the valve and the end of the hose inlet/outlets will leak out.

Pull the canister filter from underneath the aquarium and take it to a place you don’t mind getting wet, or lay down a drop cloth. Begin by unclasping the lid and removing it. Wipe down the inside of the lid and inspect the impeller chamber for debris and buildup if it is accessible.

Canister filters have many different arrangements and designs when it comes to the filter media. Most of them have a series of baskets that nest into one another. The top basket usually holds a fine physical media pad, followed by either biological or chemical filtration, then the other. The bottom basket is the main physical media that captures most of the sediment, detritus, and debris. Regardless of the exact setup, you should be able to tell which components house which filter media. The key is to remember which order the housing components are in as you remove them. It's easy to forget which basket went in first. Most of the time, it just takes longer to reassemble if you forget. However, in some cases, the filter won’t work properly, or at all, or the lid won’t fit if not reassembled correctly.

Once you remove the filter media, be sure to keep the biological filtration wet with dechlorinated water, preferably old aquarium water. Like with the HOB filter, clean or replace the physical and chemical media as necessary based on use, bioload, and how worn down the pads are. Some physical media are dense sponges that can last for years without being replaced. They are usually black and have larger spaces in the sponge. The fine, or polishing pads in the top basket may need to be replaced with every cleaning as they are more delicate.

Next, wipe out the bottom of the canister filter as some detritus and sediment will collect there.

Finally, reassemble the baskets and media. Fill up the canister filter with dechlorinated water to nearly the top. Clamp the lid back on and return the filter underneath the aquarium. Reattach the hoses and open the shutoff valve. At this point, the water in the hoses should drain into the remaining space in the canister filter. This will create a vacuum in the hoses that also pulls water from the tank into the hoses as well.

Plugging the canister filter back in will begin the priming process. Some canister filters have a self-priming button, if yours does, press it when you plug the filter in. Some older filters have an opening at the top of the return hose to pour water into after you plug the filter in. Other types of canister filters will have a manual pump lever near the base of the hoses that needs to be repeatedly engaged after the filter is plugged in to prime the canister.

Sump Filter

Easily the most versatile type of filter, the sump allows for nearly endless customization. This allows you to modify it exactly to your aquarium’s needs. The open design also allows for easy access to equipment and cleaning. Sumps in their simplest form are a smaller tank, usually made from acrylic, and sometimes glass, that fits underneath the main display tank. Water flows into an overflow box, inside the main tank, then down a standpipe and into the sump where it passes through all the forms of filtration until a pump pushes the water back up into the tank.

Sumps are sectioned off by walls within the sump called baffles. Water passes over the baffles into the next chamber where it interacts with the media in that chamber before flowing over the next baffle and into the next chamber.


Maintenance on a sump can be done on and off throughout the day, week, or month. They are so accessible, the sump can continue to function normally as you perform maintenance on the filter media.

The first chamber of the sump is normally the physical media. The water drains from the tank into either a filter sock, filter pad, or a rolling filter pad. Regardless, the physical filter media needs to be cleaned or replaced as soon as it becomes clogged enough where the incoming water starts to run over the baffle into the next chamber instead of through the media.

The second chamber may contain a protein skimmer, refugium, or biological filtration. A protein skimmer has a collection cup and should be emptied and rinsed out daily or every few days. A refugium or other form of biological filtration can be left alone for the most part.

Other chambers may include other forms of chemical filtration media resin, reactors, or auto-top-off reservoirs. Resins and reactors need to be replaced according to bioload. The last chamber houses the return pump. Most sumps will have a space in between the last two baffles before the return pump chamber where you can add a sponge to absorb detritus before it enters the last chamber. This prevents sediments from entering the return pump and clogging the impeller. This sponge should be rinsed out weekly.

As the tank water evaporates, the return pump chamber’s water level will lower first. Be sure to monitor this chamber so the pump does not run dry and burn out the motor.

Other apparatus such as testing probes and heaters should be wiped down periodically and prevented from being unsubmerged at any time.

Other Filter Types

Other types of filtration I did not mention include sponge filters, internal cartridge filters, and under-gravel filters. These types of filters are not as common, but if you find yourself using one, they are pretty straightforward and you can you always contact me for tips on how to maintain them.


A key component of keeping your aquarium clean, regarding your filter, is making sure the filter media is optimized. Spend some time experimenting with how much of each filter media type you use, when you replace it, and the different kinds available. You never know what arrangement will suit your tank the best.

  • Boodleshire LLC 2021



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