How to Clean Aquarium Filter: Basics for All Media Types

how to clean fish tank filter
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My first aquarium had a corner filter that I manually filled with floss, activated carbon, and zeolites.

And then…

As the years went by, I found the basics didn’t change much even if the filter type and design did.

These days, a lot of family members and friends ask me about how to clean an aquarium filter. I often go back to the things I learned years ago, and how they apply to the HOB, canister filter, sponge filter, and other newer filter devices.


Since all the filter media for your tank sits in one device, it’s very tempting to think you have to change it all at once.

Even though changing one cartridge may seem convenient and easy, it wreaks havoc on the ecosystem of the tank.

Regardless of the filter type you have, knowing how to change the media at different intervals is very important.

Cleaning the Outside of the Filter

Depending on the filter type, it may have inlets right on the filter body that aren’t attached to hoses. For example, corner filters and HOB filters have vents that need to remain free of debris.

Other than that, the outer housing of the filter doesn’t require much in the way of cleaning. If it is located inside the tank, you may need to wipe off algae or other deposits every few months.

4 Core Filter Media Types and How to Replace Them

zeolite media for filter

Mechanical Filtration Floss

Never rinse or remove more than 50% at a time. Beneficial bacteria colonize this floss.

When you rinse the floss, try to do so in aged aquarium water instead of tap water so that you lose as few nitrifying bacteria as possible.

Activated Carbon

If you don’t have live plants in the fish tank, change the carbon every 2 – 3 weeks, especially if the tank is new or heavily stocked. 

Once the ecosystem is established, you can do away with activated carbon. Only add it to the fish tank filter when there is smoke, pollutants, or other noxious fumes in the air.

You can also add carbon temporarily to the filter when you add new tankmates, notice changes in the tank water parameters, or need to clear out medications.


I do keep zeolites in my filter as a matter of routine, but rarely change them out after the first year.

Once the fish tank is well established, there won’t be ammonia surges unless you overfeed the fish or let debris build up in the aquarium gravel.

Change zeolites out when tests show trace amounts of ammonia in the tank. As you grow more experienced in observing fish behavior, you will recognize the symptoms of ammonia in the tank and can use that as a guide for replacing zeolites.

Other than that, you can just rinse them if they get clogged or dirty-looking.

Nitrate Reducing Aquarium Pad

If you don’t have live plants in the tank, you will need nitrate-reducing aquarium pads in the filter. Replace these every 2 – 3 months, or as directed by the manufacturer.

The Best Order for Filling Your Filter With Media

In order for debris and chemicals to be removed, water has to be moved through a medium that traps whatever needs to be removed while water passes through.

When filling up your filter with DIY media, it is very important to know how water flows through the filter. The area closest to the inlet ejection is where you need to put media for filtering out large-sized debris.

This is where you would put filter floss or anything else designed to capture dust, debris, and floating algae.

Next, you would put activated carbon, zeolites, and other chemical removal media. 

Place the nitrate filter pad in the area closest to the outlet of the filter.

If you notice clogging at a particular stage in the filter, then you can add more floss or some other pre-filter material before that stage. Try to find something that has bigger pores or spaces so that it captures larger-sized debris.

Caring for Hoses and Valves

caring for aquarium hose

Inspect valves and hoses daily to make sure there are no leaks. Clean water hoses weekly or monthly depending on whether or not sediment is building up in them.

I also recommend installing check valves on anything that may allow water to exit the fish tank.

Pros and Cons of DIY Media When Cleaning Aquarium Filter

Today, there are hundreds to thousands of aquarium filtration media products to choose from. Even though they all fall into basic material categories, it can be difficult to decide what will work best for your tank.

DIY media not made for aquariums may work just as well, if not better in some cases.


  • Usually much cheaper.
  • Offer a wider range of pore sizes.
  • Easier to cut to size or optimize in other ways


  • may contain chemicals that are harmful to fish or other creatures in the tank
  •  may break down or rot faster than media made specifically for aquariums

Fun Fact: It’s not all about fish care, too, you know! Good bacteria need to thrive in your tank to assist your pet fish’s growth and reproduction. Learning how to change aquarium filter without losing bacteria is one way of assuring a well-maintained fish tank!

Frequently Asked Questions

What are the indicators that your tank’s filter needs cleaning?

If you visually inspect the filter, you may see signs of water flowing over, under, or around the filter media instead of through it. This shows the media is clogged and needs rinsing or changing.

Other than that, just keep an eye on the water quality parameters. For example, if nitrates are rising, it may be an indicator that you need to change the nitrate absorber pad.

This may also be a sign you need to do a partial water change and add more plants, especially if aquatic creatures are getting bigger and producing more waste.

Your goal should be as balanced an ecosystem as possible so that you have to change filter media as little as possible.

Watch this video especially if you’re a beginner:

What is the best filter media for aquariums?

This depends on the creatures in the tank and their age.

For example, fry and shrimp will do best with filter sponge media. If you need to add zeolites or activated carbon to their tank, you can put them in a nylon stocking or filter socks and then place it near the main filter.

How often should aquarium filter media be changed?

For mechanical filtration media, only change it when it is too clogged up to rinse out or starts to rot.

For chemical filtration, change it based on manufacturer directions or as circumstance dictates.

For example, if you add activated carbon to clear the water of medications, you would change the activated carbon after the water is cleared up even though that only takes a few days.


I always say once you know how to clean an aquarium filter of one design, you know how to clean them all. Just pay attention to how different design aspects determine how the filtration media will fit into the device and the water flow.

Beyond that, the actual timing of media replacement depends more on the ecosystem within the tank than it does on the materials themselves.

Last Updated: July 11, 2022

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