How Does A Canister Filter Work? Best Models, Set Up, & More

    How Does A Canister Filter Work

    Of all the fish tank filters out there, canister filters might be the most intimidating for beginners. These units are large and sometimes more complex to set up and maintain. So how does a canister filter work?

    A canister filter is a pressurized canister with several media chambers inside. Water is forced inside and through each chamber. Mechanical, chemical, and biological filtration occurs inside. Removing floating particles and dissolved pollutants from the water before returning it to the tank!

    Canister filters do have distinct benefits and drawbacks. I’ll be discussing these in great detail below, to help you decide if this is the right filter for your aquarium. But if you can’t wait, this YouTube video breaks down the subject for you:

    YouTube player


    What Is A Canister Filter?

    Canister filters work a little differently from other filtration systems. Rather than sitting on or inside of the tank, a canister filter pulls water down to it. These units typically sit underneath your aquarium. But you can place one anywhere, even beside it if you want it to be easy to access.

    Sponge, undergravel, and power filters are what most aquarium hobbyists are familiar with. Canister filters are the tools of choice for intermediate and advanced level fish keepers.

    They offer the most options in terms of filtration media. And are easy to add onto spray bar attachments and other systems. Ensuring aquarium water is fully purified for optimal fish health!

    How Do Canister Filters Work?

    How Do Canister Filters Work?
    Ember Tetra (Hyphessobrycon amandae)

    Canister filters consist of an external chamber with a water pump built into it. They pull water out of the fish tank using one intake tube. Aquarium water is then pushed through several chambers with media designed to remove pollutants and floating particles.

    Canister filters are the best at providing all three stages of proper filtration: mechanical, chemical, and biological filtration.

    Mechanical filters are physical screens that remove debris of varying sizes. Cotton floss is the most common kind of filter pad. But others include diatomaceous earth and filter sponges.

    Chemical media like activated carbon works by reacting with dissolved molecules. These substances attach to the chemical media, which often needs to be replaced. Specific media choices target different chemicals in your aquarium water!

    Biological filter media provides a home for nitrifying beneficial bacteria to make their home! These micro organisms feed on ammonia, nitrite, and nitrate. The three forms of nitrogenous waste that impact fish health.

    Inside a canister filter there are several filtration media chambers. Larger filters may have enough space for six or more kinds! Once water is pushed through the filter media it is sent back into the aquarium via the lift tube.

    Best Canister Filter Models

    Best Canister Filter Models
    Clown Loach (Chromobotia macracanthus)

    Here are a few models that meet the needs of most aquarists:

    Fluval FX6 High Performance Aquarium Filter: with 563 gallons per hour of water flow and several gallons of media space, the Fluval FX6 is the best canister filter for large systems. Its rated for aquariums up to 400 gallons in volume!

    SunSun Hw303B 370GPH Pro Canister Filter Kit with 9-watt UV Sterilizer: medium sized aquariums of 55-100 gallons benefit greatly from switching from power to canister filters. Heat and oxygen exchange are all improved. As is processing of the waste released by large aquarium fish. This model by SunSun also has a 9-watt UV sterilizer bulb installed. Which instantly kills pathogenic bacteria and green water algae!

    ZooMed Nano 30 External Canister Filter: there are few options for small 10-30 gallon tanks since power filters are so popular. But the ZooMed Nano is a rare exception! You gain all of the benefits canister filters offer for smaller tanks. The media chambers offer excellent customizability. And the design is simple enough that beginner aquarium owners won’t feel intimidated during maintenance tasks.

    Marineland Magnum Polishing Internal Canister Filter: if you don’t want to deal with tubes running from inside the tank to out, internal canister filters might be right for you. This unit from Marineland also includes a fourth stage of filtration using a micron filter cartridge. These are capable of polishing ultra-fine particulate matter from your aquarium water. Clay dust, silt, and algae spores can be filtered out. The one downside is that you need to reach into the aquarium each time you want to perform maintenance on your filter.

    Penn-Plax Cascade Canister Filter: if you want the benefits of canister filters without the complexity, this model by Penn-Plax is right for you. Stacked media chambers are simple to set up, maintain, and break down for cleaning. The unit has a top-mounted pump, obvious sealing clasps, and two intake tube attachments. It can be up and running in just minutes!

    How To Set Up A Canister Filter

    How to set up a canister filter
    Spotted Cory Catfish (Corydoras punctatus)

    Setting up a canister filter need not take long. The units work similarly to power filters and other systems. The main difference is that canister filters work under your tank rather than inside or attached to the back!

    Step 1: Remove the canister filter and all accessories from the box. Account for all of the equipment listed in the instructions. Including tubing, warranty papers, water seals, and media.

    Not all canister filters come with the filter media you need. Some may have a few bags of basic media like activated carbon but no bio media or resin additions. So make sure you purchase any required media before you have to add fish to the tank!

    Step 2: Arrange your media baskets and fill them with filter media designed to fit inside them. Many canister filters require you to arrange your media in a specific order.

    For example, you shouldn’t have filter floss as the last stage. It’s designed to screen out the largest of floating particles. So you want it to be the first thing your dirty aquarium water comes into contact with. And need to place it inside the canister filter accordingly. Activated carbon and many resin media need to be rinsed first. They contain fine dust that will irritate fish gills if added to a filter dry.

    Step 3: Fill the canister filter with water. Use either tap water treated with dechlorinator or aquarium water. Once the unit is full, prime it if the directions require it. Or plug in the filter and allow it to self-prime. Priming a canister filter involves removing as much air from the lines as you can. Many units have a button that can be pressed to force air from the lines, priming the filter.

    Others will clear air from the lines by force (self-priming). If the lines are dry the integral water pumps may not be able to pull liquid from the aquarium. If your unit isn’t a self-priming model, never run the lines dry. Many filter pumps are water cooled and can overheat if run without water for very long.

    Step 4: Monitor the water flow for a few minutes. Gurgling in the lines or unit is normal and part of the priming process. This usually goes away in 15 to 30 minutes but sometimes takes up to 24 hours to quiet down.

    Also check the unit for leaks along the lid. If you see water droplets or other signs of moisture, unplug the unit and double-check the seals. It’s possible you may not have secured the fasteners that hold the unit together or have a hose connection that is loose. Any of which can rupture, causing a catastrophic release of water from the aquarium onto your floor.

    Step 5: Adjust the filtered water flow as needed. Most canister filters have adjustment knobs on the unit that reduce or increase power from the pump. Too little current may not ensure good tank turnover. Yet too much flow can cause fish to be dashed around by the force.

    Pros And Cons of Canister Filters

    Ram Cichlid (Mikrogeophagus ramirezi)

    Canister filters are top shelf options for your aquarium life support system. But there are both pros and cons to consider before choosing one.

    Canister Filter Pros

    Here are the main reasons why I recommend choosing canister filters:

    • Highly Customizable

    This is the main difference between a canister filter versus any other kind of filter. The filter media selection you can use with one is almost endless. Only sumps and other large specialty filters are more customizable.

    Canister filter media chambers usually aren’t designed for proprietary media only. If you like filter floss or activated carbon, you can add it. But you can also swap out the carbon for additional biological media. These are invaluable for ammonia removal; you really can’t have too much biological filtration capacity.

    Or you can add resin, ceramic rings, lava rock, or anything else you want. Keeping a few media chambers empty lets you slot in specialty options. Phosphate absorbers or water softeners can be used as needed without having to disrupt your usual aquarium filtration!

    • Excellent Water Turnover

    Canister filters function using some of the most powerful water pumps you can get. They pull water into the unit from great distances compared to power filters. All that force ensures that water flow completely turns over your aquarium water.

    This is most important in larger fish tanks where heat and oxygen can stagnate if there isn’t enough water flowing. These flow-less dead zones can also result in less oxygen getting into the substrate. Which causes anoxic pockets to form where hydrogen sulfide and other noxious gases accumulate. This is more common in a large fish tank with a deep sand bed, rather than gravel.

    • Discreet Filtration System

    Canister filters are one of the most discreet systems you can choose. The only obvious sections are the lines leading from the pressurized canister back into the aquarium. The rest of the unit sits under the stand, which makes them easy to hide.

    Other filtration systems will sit inside of the aquarium. Or hang on the back and sides. Which requires additional space when placing the fish tank and detracts from the overall appearance. Some canister filters are even submersible. Allowing you to hide them behind driftwood and other decorations!

    Canister Filter Cons

    As great as a canister filter is, there are a few negatives to consider:

    • Less Affordable

    Canister filter models are pricier than even the largest power filters. There are plenty of units sized for smaller tanks that won’t break the bank. But if you need the largest amount of internal space and very strong water flow? Then you will be paying several times what you would for any other filtration system.

    • Take Longer To Maintain

    Even on a smaller canister filter maintenance ends up taking longer. You have to first decouple the hoses and seal them so water doesn’t end up draining onto the floor. The unit has to be removed from the stand and opened up. Even if you only need to access one media chamber you will likely need to remove several.

    In most designs the chambers are stacked on top of each other. If you’re looking for fast maintenance and convenient access a power filter is a far better choice.

    Canister Filter VS Other Filtration Systems

    Canister Filter Vs Sponge Filter
    Dwarf Puffer (Carinotetraodon travancoricus)

    Now you understand the pros and cons of a canister filter. But how do they compare to other filtration systems for aquarium water?

    Canister Filter VS Sponge Filter

    Canister filters are in another league compared to sponge filters. Some sponge filter designs manage to incorporate all three stages of filtration media. But they are size and flow limited compared to most canister filters.

    Sponge filters are run by an air pump. The bubbles that drive water flow do provide aeration but little in the way of circulation. A sponge filter can circulate a small fish tank but don’t scale well with size.

    Canister filters have a dedicated water pump that operates with much greater force. Even larger aquariums can be well mixed by a single canister filter. Sponge filters for large aquariums are better used for supplemental filtration rather than the main unit.

    The flip side is that you can use a sponge filter for tanks that require no strong currents. Tanks for raising baby fish fry, quarantine tanks for sick fish, and freshwater shrimp breeding tanks all do well using a sponge filter. A canister filter would be too powerful for these aquarium setups.

    Canister Filter VS Power Filters

    Canister filters can be a hard sell compared to power filters. Low end models are basic in design and typically use just cotton floss and activated carbon.

    But middle to high end power filters have space inside for bio balls. And even custom chemical filtration media like ammonia absorbing resins. So which is right for your aquarium?

    Thanks to their design, canister filters ensure that less water flow can bypass the filter media. Even if your filter media starts to clog a canister filter will still force water through it. Whereas a power filter is more likely to allow water to flow right past.

    Canister filters also work better as tanks grow larger. The pumps are more powerful and able to ensure water flow circulates throughout the entire tank.

    Power filters are better if you want faster access to the filter and don’t need as much customizable media. They are innately better at aerating your tank via surface agitation as well. That said, you can still purchase a spray bar for your canister filter so it aerates the surface.

    The flip side of this is that splashing also increases your aquarium water evaporation rate. A canister filter is better at offering quiet operation by using a splash-free return hose.

    Last, power filters are more affordable and provide plenty of filtration for smaller aquariums. A canister filter can be overkill for a fish tank less than 40 gallons in volume. Too much filtration is always better than too little, though!

    Canister Filter VS Undergravel Filter

    Undergravel filters offer the fewest benefits compared to other filtration systems. They function by directing water flow through the substrate. Screening out material like a giant mechanical filter and providing biological filtration as well.

    Many undergravel filters also have chemical filtration cartridges built into the outflow. But these chambers are much smaller than the ones inside a canister filters.

    Undergravel filters are also much harder to clean. You can take a canister filter out from under your fish tank. Open it up and have the inner media bags replaced in a few minutes.

    You have to lift an undergravel filter to clean inside it. All of the fish poop and other debris gets released into your water. Fish can also get trapped underneath during this process.

    The one setup where an undergravel filter is truly effective is inside planted aquariums. Fish waste is pulled into the substrate, right where the roots of your plants are.

    The plants will then consume nitrate and other byproducts of decomposition. This enriches their growth and keeps you from needing to lift the undergravel filter for cleaning!


    Betta Fish (Betta splendens)

    Canister filters offer endless ways to process aquarium water. They excel at customizability, media chamber volume, and overall water flow. Many even have additional features like UV sterilizers and maintenance timers built into them. Any serious aquarist will get great value out of a canister filter, even for a smaller fish tank!

    Recommended Reading:


    Don’t miss out on valuable tips! Subscribe below for our newsletter and get weekly updates on newly published posts.

      We respect your privacy. Unsubscribe at any time.