When to clean your canister filter

When To Clean Your Canister Filter – (Finding Your Schedule)

You should definitely have a schedule for when to clean your canister filter. Whether that’s every month, every 3 months or every 6 months.

When you do clean your canister filter take note of the date, right it down, post it on your fridge, send yourself an email, whatever and then stick to that schedule as long as everything is going well in your tank. But the question is how do you set that schedule to begin with, how do you know when to clean your canister filter.

When To Clean Your Canister Filter

I know this can be a struggle for many beginners in the hobby, should I shouldn’t I? Is the tank cloudy because the filter’s dirty? Are the fish ok, should I wait until next weekend, I’ve been there trust me and I know it isn’t fun. Would be nice if your canister filter just sent you a text like “CLEAN ME 😡”

Seriously though, the first sign that its time for you to do a filter cleaning should be your flow rate! Is your output flow strong and steady like when you first set up your filter, or has it slowed down?

Filter Output Flow Rate

When you notice your flow begin to reduce that is a good sign you should consider doing a filter cleaning. Your flow is reducing because the gunk in your filter is piling up, your sponges are getting full of detritus and water is having a hard time getting through them and back out to your tank. Which means its time to clean those sponges.

So if you see a reduced flow from your filters output, start preparing for a filter cleaning.

Examining Your Canister Filter

Once you’ve decided to go ahead and pop that bad boy open now is the time for you to examine your filter and determine just how dirty it is. If it looks disgusting, like bugs and maggots have been fornicating in paradise… then… you waited too long to clean your filter. However long its been since your last cleaning it was too long. Next time do it sooner, much much sooner!

And if its your first cleaning on the filter now you know for next time, don’t wait that long!

But If you pop it open and things look pretty clean, like white sponges are still white, water in the canister is relatively clear, then you’re cleaning is too soon. Most canisters can go longer than you think without needing a full cleaning, they’re designed this way so don’t be surprised if you open it up and its really not that bad.

You can still go ahead and clean it at this point since you’ve removed it from the tank and opened it already, but make note of how long you waited since last cleaning and next time push it a week or 2 longer before your next cleaning.

Finding Your Sweet Spot

This is the trick to finding your sweet spot. Eventually you’ll determine how long it takes for your filter, on your tank, with your bio-load, to need a cleaning. So how should your filter look if the timing is right?

What you want to see is brownish sponges and even some detritus floating around in the filters water. When you squeeze the sponges out the water should be brownish as well.

But you don’t want to see any waste on your bio media. If detritus makes it through your sponges and onto your bio media it will clog its pores preventing beneficial bacteria from growing on it. And that defeats the purpose of the bio media.

This can cause what bacteria you do have to die off causing ammonia spikes…and if you didn’t know, an ammonia spike is the fastest way to kill your fish.

Cloudy Tank Water – Clean Your Filter

One more clear sign that its time for a filter cleaning would be a dirty or cloudy looking tank. But if you’ve been consistent with your water changes, vacuuming and following all the best maintenance practices but your water still has that dusty dirty cloudy look it could mean 1 of 2 things.

  1. Your fine mechanical filtration and/or your chemical media may need replacement.

Fine mechanical media will get clogged up and need replacement much sooner than your filter needs an entire cleaning. Chemical media in general needs replacement about every month or so. Specifically when using carbon, when carbon is full and cannot absorb anything else it will began to release what it has absorbed back into your water.

2. Your filter needs a cleaning.

Replacing the fine mechanical media is one thing. But once your course and medium sponges are full to capacity stuff is going to get through. Through to your bio-media which we already discussed is a bad thing and also all the way through your filter and back out to your tank. At this point you’ve essentially just created a recycle of your dirty tank water…no Bueno.

This seems like a good time to mention why placing your chemical media in the top-tray of an FX6 is a good thing.

Chemical Media In Top Tray of FX Series Canister Filter

Yes, most of us know that the order of media is always the same. It’s mechanical, then bio, and finally chemical. Well the way the FX series of canisters are designed that would mean that your chemical media has to go in the bottom tray.

But like we just went over you’ve got to replace your chemical media much more often than you’ll need to clean your filter. So opening up your filter, pulling out all the trays, separating them and digging to the bottom to get to that chemical media is disturbing a lot of beneficial bacteria in your filter.

Maybe even some potential anaerobic bacteria that is super hard to grow in a canister, but by messing with it so often you definitely wont grow any anaerobic bacteria. Which btw is the kind of bacteria that helps in reducing nitrates, very beneficial!

So by placing the chemical media in the top tray along with your fine mechanical media it can be very easily accessible for replacement.

Now I know what some of you are thinking. No, having the chemical media before the bio-media will not prevent beneficial bacteria from growing on it. Plenty of ammonia and nitrite will still make it to your bio-media for the beneficial bacteria to feed on.

How do I know, because not only was this awesome tip given to me by a veteran of the hobby and what I consider to be a master fish keeper, I’ve also tested it myself.

I would never suggest anyone try something I haven’t tested myself and I can safely tell you this method works perfectly fine, your tank will remain cycled and every month replacing that chemical and fine filter pad is a breeze!


Once you’ve found that sweet spot, where your filter is perfectly dirty enough, but not too dirty…now you know how long you should wait in between your filter cleanings.

As an example on my 210 gallon over stocked African Cichlid tank I run 2 fx6’s and I alternate their cleaning every 3-4 months.

Meaning every 3-4 months I clean one and next 3-4 months I clean the other. That means that each filter might have a 6-8 month swing in between a cleaning!

As long as everything remains the same in your tank and you aren’t having any water quality issues you should try to keep your filter cleaning schedule the same, or as close to it as possible.

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