Troubleshooting Aquarium Filters

Is your filter making noise? Does it rattle? Squeak? Is it struggling to suck up water? Has the output dwindled to a trickle? Is it not working at all????

Most filters are pretty simple at heart no matter how many trays or levels or compartments they have inside. Most of them have only one moving part. That is the impeller, which resembles a small propellor or fan. One exception might be a filter with a bio-wheel. I’ve not ever used one of these, but anything that moves can potentially make noise. So a bio-wheel may be a noise source and it can get stuck too.

Whether or not you can get replacement parts for any given filter should very much be a part of your considerations when you buy one, since, at some point in time, every impeller will wear out and need to be replaced, even if nothing else does. Many brands do not offer parts.

Reasons why your filter may be making a lot of noise and how to fix it:

1. An obstruction of some sort that’s jamming the impeller. Check the impeller and the shaft it rotates on, and the well that it sits in, if it has a well. Not all impellers sit in a well, but many of them do.

If the impeller is not moving, it may simply need cleaning. Or it may need replacing. Impellers can get clogged with a simple buildup of biofilm and slime. Sometimes sand or small bits of gravel or a tiny snail will make it inside and jam the impeller. That can make a very loud sound. It can also damage the impeller so badly it will have to be replaced.


Disassemble the parts so you can remove the impeller. Clean the impeller well and the impeller with a narrow soft brush or Q-tip. An old toothbrush works nicely for an impeller. Then put it back together and test run it. If it still makes noise or fails to move, then either the impeller itself or the impeller shaft, or both, probably need to be replaced.

Not all filters will have replacement impellers available, but modern technology may yet save the day. If you can get to a 3D printer, you can make a replacement ‘prop for an impeller.

The impeller shaft would be much tougher to jury rig as they’re usually made from metal and a very specific size. If no replacement can be had, a very thin coat of Vaseline or mineral oil may help an impeller shaft that is worn keep going for awhile longer.


2. Sometimes a lid can vibrate and make an annoying sound. If the lid is properly seated, this should not happen unless it is a very cheap filter, or some part has warped or been damaged.

Solution A small weight on the lid may help - or run some silicone around the lid on the underside to help cushion it. Or take a small file to it and file down any protrusion that may affect the fit.

A small weight on the lid may help - or run some silicone around the lid on the underside to help cushion it. Or take a small file to it and file down any protrusion that may affect the fit.


3. If the filter is badly clogged with dirt and organic matter because the media needs rinsing, that can also cause noise.


Remove the media and any media holders, rinse it all very well in old tank water and put it all back.


4. Pinholes or other damage to an intake tube can also cause noise. If the uptake is vertical, any damage may break the partial vacuum in the tube and make a lot of noise or simply fail to suck up water. Pinholes or breaks from being bent, in one spot or too often, can cause problems with flexible tubing as well, such as leaks or failure to suck up water.


Check every tube closely for damage of any kind or pinholes or chips.

Crazy glue might work to close a small hole, or to affix a patch over it. There are some other adhesives that are also safe for potable water, and if it is safe for potable water it is also safe for fish tanks and filters. You might try silicone. You can also try on of those nifty new kits from Bondic, that fixes many things using a liquid resin that cures in seconds with UV light from an LED in the kit.

But, a new tube may be the only permanent solution.


Reasons why the filter might not be working correctly and how to fix it:

1. Slower than normal output from the filter or just a trickle


Check the intake tube end. Plants, snails, mosses and various other debris can easily block up the intake, to the point it can barely suck up water at all. Remove anything clogging the intake’s end and it should be ok.

If the intake tube has a sponge cover on it, that can become severely clogged and impair the flow severely. Remove the cover and squeeze it out very well in old tank water, before you put it back on.

Check the media inside the filter. If it’s very dirty, it is also clogged and that can greatly impair the flow of water. Sponges especially can get badly clogged. Remove the media, all of it. Rinse well in tank water. Put it back.


2. The lid is being pushed up off the filter.


Almost always due to very dirty, clogged media. Remove the media and rinse well in tank water before you put it back. Media touching the edge of the box will often wick water over the edge making it look like the filter is leaking, when in fact, it’s not.

Media may also rise up if you stuff too much media into a filter box. It can also slow the flow dramatically or push water out in spots other than the intended output.

If you added extra, remove it and see if that fixes the problem. If you changed from cartridges to bulk media cut to fit, reduce the amount or resize the pieces.


3. The filter appears to be leaking


Take it apart and dry it off. Check for obvious cracks or holes. If none, [our in some water and check for a leak location that way. It may be possible to repair or patch cracks or holes. Epoxy can work. Silicone may work. Sometimes Crazy glue will work to affix a patch on the exterior but don’t expect it to work on the inside where it will always be wet. Some plumber’s two-part epoxies are safe for potable water and would work for this purpose.

Make sure nothing was touching the filter near the top, as that may cause wicking, which can appear to be a leak.

Make sure your HOB or exterior canister is level! If it is tilted, it may leak, thanks to an uneven water level.

Check any seals or O rings.Such as those around a motor like the ones you find in an Aqua Clear filter. O rings, seals, or gaskets do wear out and cease to control leaks. Replace them if that’s the problem.


4. It still doesn’t work?

You have tried most everything else and you still have a noise or a malfunction or it simply does not run.


I would take the device apart into every single piece it has. I would examine every piece for any damage or holes. Hold them up to a strong light to check for tiny holes or fine cracks. I’d thoroughly clean each piece and then, if I found nothing I could repair, I’d reassemble it and test run it. Often, disassembly and reassembly will be all it takes. Usually, any noise will be resolved.

If, after all that, your filter will not work at all, then chances are pretty good that you need a new motor. You’ll have to check and see if one is available.

Image posted by Carley

So... what do you think? Please leave me a comment.


  • Vale: Good tips for troubleshooting!
  • Fishfur: Thanks. Almost all my filters were purchased used. Most of them worked, but many also had minor problems and sorting those out was something I had to learn very early on.
  • Vale: It’s a good thing you learned how to look for the source of the problem and figure out how to fix it because I think many people would just throw it away even when it just needed a little bit of work!
  • Fishfur: I was raised by a very frugal mother and a DIY dad. We never tossed anything if there was a way to fix it!
  • Vale: I wish more people were like that :)
  • MarkDiaz: Nice blog!
    Some canister filters have a one-piece connection for both hoses. Some have separate connections. If you get them backwards reconnecting them in the low light inside of cabinet type stand, the filter (obviously) will not work. I put a piece of white tape around the inflow tube and the same tape on the filter near where it is supposed to be connected. Makes it easy to see what to connect to where.
    Used similarly a piece of colored tape near the end of each electric cord. Yellow for lighting, red for the heater, blue for the filter, white for the air pump. Makes it easy to tell what you want to unplug when you need to.
  • Vale: MarkDiaz, that’s a good idea to help organize!
  • critterchic: LOL, my daughter recently told me her filter wouldn’t work after she cleaned it. I asked if she had cleaned the impeller and its hole. "The WHAT?"
    Had to show her the hidden parts, not the obvious media compartments. Pipe cleaner in hole, gentle sweep of impeller blades and good to go.
    I hope your blog helps people figure out how to fix instead of toss.

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