How to configure an external filter

Canister filters are great, aren’t they? Powerful, pressurized water filtration that makes your water crystal clear and the almost limitless possibilities to customize the filter media you use can’t be beat, right? But there’s another thing that owners of external filters can also agree on: the instructions that come with the filters can sometimes be terrible, and the setup is often the hardest part, especially for beginners.

How are you supposed to get your filter to work properly without instructions? Are you up to date in the preparation of the aquarium? How to set the external filter media? Where to put your filter? Do you know how to cut your hoses or connect them to your boat and take them to your tank? It is a complicated process and it is easy to miss a step. Fortunately, the Internet (and yours for real) are here to show you how to set up an external filter.

What you need to start

It goes without saying, but you’ll need your filter, your components, and all of your media to get started. The exact components that come with your particular filter may vary, but in general, you will have the following:

  • hoses
  • A motor
  • tank connectors
  • clamps
  • hose clips
  • intake assembly
  • outlet assembly
  • filter bowl
  • Media trays or baskets
  • media bags
  • foam inserts
  • ceramic rings
  • Activated carbon

generic hoses

Standard hose can sometimes be stiff and unwieldy. You want the tube to be thick, but it still needs to be flexible and free of kinks. Instead of ordering a brand name replacement tube for the filter, I like to go with a roll of generic vinyl tube that can be cut to the length you need. It’s less expensive, generally less messy than working with the tube that comes with your filter, and you’ll have a lot more on hand in case of an emergency.


Depending on your filter, it may come prepackaged with ceramic rings as the primary biological filtration media. Some people prefer bio-balls, however, as they break down much more slowly.

phosphate removers

Activated carbon is a popular medium for chemical filtration, but I prefer to add some phosphate remover as well to help control algae growth in my aquarium.

extra foam

Your filter may have come with a type of foam infill for mechanical filtration, but to optimize your results, it should have a combination of coarse foam, fine foam, and extra-fine foam.


1. Identify your parts

Unpack everything, get your filter parts list, check that everything that should be there is there. Your filter should come with everything you need to start pumping. If your filter came with media, you’ll want to check it to make sure it’s not damaged and is suitable for use in your filter.

2. Prepare your tank

Find a good place for your filter to rest. Remember that your filter should be under your aquarium for optimal use. The ideal position for most filters falls between 8 inches and 4 ½ feet below the water level in your tank. Check your filter guide to find yours. You’ll also want to make sure your aquarium is filled to its maximum level and that your hose can follow a direct path to your tank. You don’t want any loops, slacks, or kinks in your tubing, so test your tubing before you set it up to make sure it can get to the tank without a problem.

3. Prepare your filter

Now we begin the process of preparing our media for the filter. Remove filter motor head and make sure all media baskets are inside. Depending on your filter, you may have 3 or 4 baskets to fill. Gather your favorite media, sort it by type, and get ready to install it layer by layer. If you have any space at the bottom of your filter when the baskets are inserted, consider lining the bottom with some old ceramic rings to diffuse any debris that collects there.

4. Install mechanical means

Your mechanical media should be placed in the first tray of your filter. Why? After your filter draws water from the tank, it flows from the first filter tray and is then forced into the other layers, getting cleaner with each pass. Mechanical filtration should be the first step in this process, so that when the water reaches the biological and chemical stages, the filter media is not clogged with debris and debris. Take your 3 foam varieties: coarse, fine, and extra-fine, and stack them on the tray from bottom to top in that order. Each layer will filter smaller and smaller particles, preparing them for the next stage of the process.

5. Install biological media

You should add your preferred biological medium to the second tray from the bottom. As mentioned, some tank owners like ceramic rings, others prefer bio-balls. Others still prefer to use something known as Biohome for all their filtration needs and skip mixing media altogether. You may choose to store your biological media in filter bags, but there are many tank owners who simply cover their trays with the biological media, to no ill effect.

6. Install chemical media

Your third and fourth pans (if you have a fourth pan) are free so you can mix things up. You are free to use them for more of the same media if that makes you feel more comfortable. You can also experiment and try adding some chemical mediums to the mix. Activated charcoal is a popular option, as are phosphate removers like PhosBan. These media often come as loose granules, so if you choose to add them, it’s very important to use a filter bag (outside the bag, the granules can begin to shift and potentially clog your filter’s impeller).

7. Prepare the intake

Now we can prepare our inlet, the part of the filter that draws water from the tank. Some filters have a connector that connects to the tank and holds the hoses in place. Attach the connector to the tank. Next, connect the hose to the filter by loosening the inlet clamp, attaching the hose to the inlet valve, then tightening the clamp again.

Run the hose to the tank, cut to length (no slack, no loops), then secure the hose to the connector. The end of the hose should be attached to an inlet pipe that goes down into the water in the tank. If your manual doesn’t have a recommendation on how far the tube should extend into the water, fall back on the 3-inch rule, which advises keeping the end of the tube at least 3 inches from the bottom of your tank.

8. Prepare the exit

This will be done in the same way as our preparation for the intake. Set up the tank connector, connect your hose to the filter, measure and cut, then send your hose to the tank. In this case, however, our outlet nozzle should rest at least an inch below the water line, it doesn’t have to go all the way to the bottom of the tank.

9. Start your filter

This can vary from filter to filter. Generally though, you’ll want to check that everything is connected securely and in the right place. Make sure your valves are open so the filter can draw in and then expel water from your tank. Some filters will require you to have water in the container to start, so make sure there is the necessary amount in the chamber before you begin. When you’re satisfied everything is ready, plug in your filter.

If it has an auto-priming feature, the filter will run for a bit to get the water flowing, then it will turn off to force excess air out of the bowl, then it will run continuously until you turn it off. If you have a priming button for your filter, you may need to pump it a few times to get it to work.

10. Watch your tank get cleaner

Watch your filter in action for a moment and make sure everything is running smoothly. Some filters may make rattling noises during startup. However, if these noises persist, you may want to check to make sure there is no debris clogging any of the filter components. Watch your flow rate. If it appears to be lower than expected, you may need to tighten the hose connections or remove blockages from the pipe.


It was not funny? Hopefully you are now a bit more knowledgeable about setting up your external filter and some basic operating procedures. As I mentioned, the instructions that come with many filters aren’t always the clearest or easiest to follow, so it’s helpful to have a step-by-step guide that can break down some of the hard-to-decipher language into easier terms.

What do you think? Were these steps helpful in breaking down the filter setup process? Any additional steps or tips that you think should be included? Let me know what you think in the comments and remember to share the article if you found it useful.

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