How To Clean A Fish Tank Filter – Easy Step By Step Guide

    How to clean a fish tank filter

    A clean filter is as important as a clean tank. After all, it is the life support system of your aquarium. So how to clean a fish tank filter?

    The best method for filter cleaning is to use tank water or treated tap water. Don’t use soap or other harsh cleaning supplies. Save your biological media and replace the chemical and mechanical media, if necessary.

    Use brushes or sponges to scrub away any biofilms or hard deposits. Then refill the filter with tank water and plug it back in!

    This method is simple to do and should only be done if your filter is no longer flowing properly. Are you a visual learner? This YouTube video breaks down the process in an easy to follow format:

    YouTube player

    How To Clean A Fish Tank Filter

    Cleaning an aquarium’s filter does not take too many tools. Here is what you need to get the job done:

    Step 1: Unplug your filter from any power sources and move it to your cleaning area. This might be a countertop, table, basement sink, or even an outdoor porch! Keep an eye on your heater and any other equipment that is still plugged in. If the water level is low, it’s better to unplug the heater. These devices are dangerous if the glass gets dry. A splash of water can cause the hot glass to shatter, possibly electrocuting you or your fish.

    Step 2: Open the filter housing, making sure not to spill dirty water across your working space. This water can be drained away or fed to your house plants (if any). Remove the filter media and throw it away (mechanical and chemical media) or set it aside in a small container of fish tank water (biological filtration media).

    Step 3: Scrub the media chamber using your scrubbing sponge or cleaning brush. A sponge will be enough for soft biofilm or bacterial mulm. But a cleaning brush with stiff bristles will be necessary for green spot algae, limescale, and other tougher deposits. Coralline algae and limescale may also need softening using pure, scent-free cleaning vinegar. Don’t use any scented products as the additives may be poisonous to your fish!

    Step 4: Rinse the filter and your cleaning tools in old tank water or dechlorinated tap water. Never use tap water straight from the faucet as the chlorine and chloramine are toxic to fish and bacterial growth.

    Step 5: Replace your mechanical and chemical filter media with fresh material. Cotton floss and activated carbon should always be thrown out and refreshed. But some types of mechanical media can be rinsed and re-used, such as tough polymer mesh. Rinse any new activated carbon since it is full of reactive black dust. This dust will irritate fish gills if added to a filter while still dry.

    Filter sponges can also be re-used as long as they are mostly whole. Eventually filter sponges will decay and start to develop holes. Meaning it’s time for a new sponge. They can also become coated with algae or mold, which plug holes and reduce the water flow rate.

    Step 6: If necessary, gently rinse your biological filter media with tank water. Only do this if the growth is so heavy that water flowing into your filter is impeded. The brown color and earthy smell are a sign of a rich colony of beneficial bacteria. Destroying them will partially reset your nitrogen cycle and possibly lead to new tank syndrome.

    Step 7: Scrub any tubing and filter intake covers (these often collect fish poop, string algae, and other dirty bits). If debris is caught inside you can use a pipe cleaner set to reach deep within.

    Step 8: Replace your biological filter media and refill your aquarium filter with tank water. Replace any tubing and filter intakes you removed.

    Step 9: Plug in your filters, priming the unit by adjusting the water level as needed. You may need to adjust the magnetic impeller, which sometimes get stuck when you unplug them. External filters are prone to this after a cleaning.

    Step 10: Monitor the unit for a few minutes to ensure that your aquarium filter is working properly. Unplug and adjust it if any problems arise!

    Should You Clean A Fish Tank Filter?

    Should you clean a fish tank filter?

    Now that we know how to clean your aquarium filter, let’s talk about the benefits and drawbacks.

    Cleaning most important pieces of equipment is a good thing in the pet hobby. But aquariums are more complex due to how living organisms form the backbone of your biological filtration system. Too much cleaning can actually do more harm than good!

    Pros Of Cleaning An Aquarium Filter

    Thinking about cleaning your aquarium filters? Here are the pros:

    • Better Water Flow: water flow is often impacted by the growth of aquatic organisms. These are a sign of health in most cases. But they may cause your filter to gum up. Reducing its ability to process aquarium water and remove pollutants. A good clean will also ensure your water remains properly aerated.
    • Cleaner Appearance: hoses, tubes, and other filter equipment tends to get dirty over time. Many filters are also made of clear plastic, which allows viewers to see the gunk that accumulates inside. A clean filter looks more presentable when looking at the tank. A filter coated with green algae and mulm may work just as well. But the unkept appearance is detracting from the overall aquarium aesthetic.
    • Refresh Chemical And Mechanical Media: when you clean your aquarium filter you might as well change the filter media at the same time. Biological filtration uses media that you replace very rarely. But the other two kinds of media wear out over time. In most cases, change the chemical and mechanical filter media every one or two weeks. I do this when performing my weekly water changes!

    Cons Of Cleaning An Aquarium Filter

    As good as the benefits are the cons of fish tank filter cleaning are worth noting:

    • Loss Of Beneficial Bacteria: your beneficial bacteria are more than simple germs. They form the backbone of the aquarium nitrogen cycle. To briefly summarize, these bacteria feed on ammonia and nitrite. Converting it into nitrate, which is much less toxic and can be removed during water changes. Deep cleaning a filter will kill all of them. Which will cause ammonia levels to rise unchecked, possibly killing your fish.
    • Time Consuming: even a small fish tank filter can take half an hour to clean. If you use a canister filter or other larger unit, expect an hour or more to get it functioning properly again. If you have no other choice, then perform a deep cleaning. But it’s still not something to do often. Or even every few weeks.

    How Often Should You Clean A Fish Tank Filter?

    How often should you clean a fish tank filter

    Completely breaking down a filter to clean it is not something you should do often. It causes too many of your bacteria to die. And it doesn’t benefit your system all that much.

    I only recommend undergoing the complete cleaning process when the water flow rate is negatively impacted. This can be due to excess bacteria growth. Or it can be caused by other forms of aquatic life.

    Coralline algae is not a problem for a fresh water aquarium. But saltwater tanks have to deal with it all of the time. These red algae form hard pinkish crusts that coat everything in the tank. Including aquarium filters, clogging up tubes and flow outlets.

    Coralline algae is too tough to be wiped away. So you may need to clean your aquarium filter to remove it. This can be done on a yearly basis. Or even every other year; coralline algae (thankfully) has a slow growth rate.

    Preventing Frequent Fish Tank Filter Cleaning

    Now you understand just how laborious a filter clean can be. So how can we limit the number of times we have to wash a clogged filter?

    If you perform aquarium maintenance on a regular basis, a clean filter should be the norm. It’s when you allow media to get clogged and skip water changes that a filter starts to get dirty.

    Aquariums that are overstocked with fish are also more time consuming to clean. Fish are the source of all pollution in the tank. More fish means more food and more poop.

    Under stocking an aquarium is my recommendation. It’s far easier to keep a tank clean with fewer fish. What fish you have will eat less and have more space to roam in as well!

    Can You Reuse A Fish Tank Filter?

    Most of the time you don’t need to completely throw out a fish tank filter. Filters are made to run for months to years. Sponge filters may only last a year or two, depending on the quality of the sponge. Fortunately, a new sponge is easy to find and purchase.

    A canister filter or power filter will last many years. The internal pump uses quality components that wear gradually. Even a cheap power filter’s magnetic pump will last several years. And the plastic housing shouldn’t crack or degrade for just as long. The only thing that needs replacing are the various media you add to it.

    If you keep a filter in storage for several years, components may wear out. Always test a used filter by running it for a few days before adding fish to the system. Adjust the flow controls, check the stability of the magnetic impeller, and ensure the tubing and housing has no cracks.

    An old canister filter with a hidden crack is especially dangerous since these sit under the fish tank stand. A slow leak can cause your entire tank to drain before you realize the source.

    Otherwise an aquarium filter is entirely reusable and should not be thrown away. You can even move a fish tank filter from one aquarium to another as needed. In fact, using an old filter on a new aquarium is the fastest way to get it cycled.

    You can add ornamental fish right away since the nitrifying germs inside will immediately start processing nitrogenous waste.

    Does Cleaning The Filter Kill The Good Bacteria In The Tank?

    How to clean aquarium filter without killing bacteria

    Cleaning your fish tank filters does kill some of your beneficial bacteria. Unfortunately there is no way around this. The flip side is that your tank is home to billions more. All just waiting to start reproducing again to feed on fish waste.

    Therefore we need to balance cleanliness with biological activity when cleaning a filter. That’s why you should not use soap, hot water, bleach, or other strong cleaning products. All that’s required are light cleaners, brushes, and plenty of elbow grease!

    Sometimes a deep filter clean is necessary. Maybe you’re breaking down a fish tank for good. Or a component deep within is coated with limescale or coralline algae and won’t operate properly.

    How can we save some of our bacterial life and keep our nitrogen cycle intact?

    Before you begin cleaning your filter, take a bucket and fill it with tank water. Place your biological media inside, as well as any mechanical media that’s not too worn out. These are where your good bacteria live.

    As long as these stay safe, you can limit the harm done to your microbial ecosystem. Deep cleaning will still cause some stress but reusing these components will jump-start the cycling process again!

    What if you’re only reading this after having purged the microbial life from your filter? You can reseed your aquarium using bottled beneficial bacteria. These are the same microbes that would normally take several days to a week to reestablish.

    If you have multiple fish tanks you can also take media from one filter and add it to another. Jump-starting the cycling process to prevent ammonia levels from rising too fast.


    As long as you maintain a regular cleaning schedule, you should not need to do a complete filter cleaning. Soap, bleach, and other products do more harm than good. Stick to brushes and rinsing to preserve your beneficial microbial life. And always save your biological media to maintain your aquarium nitrogen cycle!

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