How to Clean an Aquarium Filter

Filters help clean and purify the water in your fish tank, but unfortunately, the filter cannot properly do its job if it’s clogged with filth.

When and How to Clean your Filter

When should you clean your aquarium’s filter? Well, when it is dirty of course, but you should wait at least a week from the last time you cleaned the fish tank. That way your fish will have had time to adjust to his new environment before another shock to his system happens with the disruption of his water and routine.

The second thing to remember about cleaning your aquarium filter is that the cleaning method you should use depends on the type (or types) of filter that you have. This should be fairly obvious to you just by looking at your filter, but be sure to consult the owner’s manual to make sure there are no specific directions on cleaning for your particular model. Then look up your filter type below and get started.

Cleaning Mechanical filters

If you have a mechanical filter, you will most likely have a sponge or pad that sits inside it. This is the main component of the filter that you will need to clean. Here’s how:

1. Siphon or scoop out some water

You will need about two cups of water from the tank to use to clean the filter’s sponge. For the benefit of your fish, you will want to use existing tank water, not tap water or distilled water. Sure the filter may not smell as clean and fresh, but your fish will be less sensitive to the change. Use your siphon, plastic cup, etc., to remove as much water as you think you’ll need. Drain it into a medium sized bowl, like a small mixing bowl, or drain it in a bucket and transfer it to the bowl.

2. Unplug the filter

This step is pretty self-explanatory. Unplug your mechanical filter to avoid shocking yourself as you clean it. Then take it off of your tank if you can. This will make your life a lot easier. To save your floor, you will want to have an awaiting bowl, bucket or sink.

3. Clean the sponge or pad

Since you’ve already got your bowl of water assembled, this step should be relatively quick and painless, which is good, since you don’t want your fish to be filter-less for long. Simply wash all of the gunk off of the sponge with the water and your hands. If touching aquarium water is too icky for you, either wear gloves or recruit a friend to do it for you.

*If your sponge or pad is horribly dirty, feel free to replace it. But do not do this unless you feel it’s absolutely necessary.

4. Scrub the casing and tubes

Use the leftover water in the bowl to clean the other parts of the filter, or grab a little more from the tank if the water in the bowl is too dirty. You can scrub any hard to reach spots by using a filter cleaning brush, which you can find at most pet supply stores.

5. Put the sponge or pad back

That’s it. Now return the sponge or pad to the filter and return the filter to your fish tank. Pour any remaining water from your cleaning project inside it, if it isn’t crawling with gunk, that is, and turn the filter back on.

Cleaning chemical filters

If you have a chemical filter on your tank, the only cleaning it really needs is for you to swap out the carbon on a regular basis, say once a week or whenever the water seems cloudy, whichever comes first. Just follow steps one, two and four from above. Remove the carbon before you start step one and replace it with the new carbon when you’re done, right before reattaching the filter to the tank.

Cleaning biological filters

Since you want your biological filter to be filled with lots of delicious and tank skimming bacteria, you don’t want to clean it much. If you do need to clean it, just give it a quick once over with water from the tank. Follow steps one, two and four from above. Then put the filter back of course.

*As a final step, make sure it is functioning properly. If it’s not, check for clogs. Still not working? Check the owner’s manual or call the manufacturer.

Keeping your aquarium filter clean

Aquarium filters don’t really stay clean as a rule. Their whole raison de vivre is to get the gunk and pollution out of your fish tank. Therefore they will always require cleaning on a regular basis. The rule of thumb for the specific filter types is as follows:

Mechanical filters: These filters need to be cleaned the most often of the three types, at least once every four weeks. You will want to schedule your filter cleaning days so that they are several days removed from your weekly or biweekly regular tank cleanings.

Biological filters: Replace the carbon when the aquarium water turns cloudy, or at least once every two months.

Chemical filters: Give the chemical filter a good cleaning out when it appears to be clogged, malfunctioning or working very slowly.

More frequent cleanings may be needed if your fish is sick. Ask a veterinarian or aquarium store employee for advice during these times.


  1. Hello,
    I have a Tetra IN 300+ filter and it just suddenly stopped working. It hasn’t been working for a couple of days. I thought there might be a blockage in it, so I took one of the pads out of it and they were covered in filth! I cleaned them, put them back in the filter, put the filter back in the tank, turned it on and it still isn’t working! PLEASE help!

  2. After a 30 gallon filter is all clean, how do you get it flowing if it has a top of the tube before the pump valve? Won’t start pumping water.

  3. I have cleaned my filter, but it’s still not working. Whats wrong?

  4. Most causes of filters not working is a clogged impeller. Check that and give that a good clean. Any tubes you have may be blocked too.

  5. Warren,
    That hapens to me sometimes. Get a long hose, fill it with tank water, and blow it up the tube; while it’s going, there’s too much air… even my primer button can’t do it sometimes. If you have a water flow restrictor on a canister filter, shut it right off before you flick the switch and the water will stay in the hoses and not drain back to the tank; saves lots of dramas.

  6. I’m a new fish owner and have cleaned the filter with tap water (I now know this is wrong). Will this harm my two fish? I put a tiny tiny drop of Tap Safe in, and am going to bed now. I hope they will be ok. Any advice???

    Thanks, Sherry

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