Why Does My Aquarium Filter Keep Clogging?

Last Updated on December 11, 2021 by cmoarz

Everyone is always telling you your filter should only be changed out every few weeks to a few months. But for some reason, your filter is always clogging up. Why does your aquarium filter keep clogging like that? Why Is My Aquarium Filter Getting Dirty So Fast?

There are actually quite a few reasons your aquarium filter may clog prematurely. The first, and most common reason is that the filter is simply too small for your tank.

If you have a small tank, you need a small filter, and if you have a large tank, you need a large filter. Trying to use a small filter on a large tank is a recipe for frequent filter cleanings.

Overfeeding can easily cause a filter to clog prematurely. If you’re not careful with how much food you put in, your tank can quickly have a major issue with it. Turning off your filter during feeding times can help reduce this issue considerably.

Algae blooms can be just as bad for your filter as overfeeding. Too much algae in the tank can quickly plug up a filter and cause it to work overtime. This is one of the reasons many people choose to use an algae-eating fish such as the Plecostomus.

A planted tank can also increase the frequency in which you must clean your filter.

Plants that break off, Rot away, or get chewed off will often find their way into the filter. Sometimes they even block the intake completely.

Duckweed and other floating loose plants are especially bad for this. The flow of water pushes the duckweed down into the filter intake on certain models. If it is not caught in time, the filter will be clogged and working overtime.

Fragile plants, such as guppy grass that break up if you look at them the wrong way are a surefire way to clog a filter as well. This can be avoided by adding a thin layer of filter floss to the intake with a rubber band.

This floss will prevent large and small debris from getting into the filter and clogging it up prematurely.

You will have to replace the filter floss every time it starts to get clogged, But it’s much easier and faster to do than cleaning out the filter media itself.

How Do I Stop My Aquarium Filter From Clogging?

You can prevent your filter from clogging too quickly by doing proper maintenance to your tank on a set schedule. Vacuuming gravel, trimming dead or overgrown plants (turn filter off first), and cleaning up excess algae and other growth around the glass.

Being careful to not overfeed the fish in the tank can cause excess debris that will clog the filter.

Putting a ring around the filter output to prevent the water from pushing duckweed and other floating plants into the intake.

Utilizing filter floss as an extra measure on the intake to stop large and small debris from reaching the filter.

Replacing the filter floss as needed to keep it from getting clogged.

If you are still having problems with your aquarium filter clogging, you may need to upgrade to a larger model.

Remember, a filter is only as good as the size of the tank it is running on.

Replacing the filter media on a routine, scheduled basis will ensure that your filter keeps pumping away while keeping debris out of your tank.

Keeping this scheduled maintenance up to date will go a long way toward making sure you don’t have an extreme clogging issue in the future.

What Is the Brown Stuff in My Aquarium Filter?

That brown muck you find in your aquarium filter is broken down organic debris; the result of decomposing fish waste, plant matter, or uneaten food as it’s broken down by beneficial bacteria.

The smell should be earthy. If it smells foul and disgusting it could be a symptom something is wrong somewhere in the tank.

It’s not anything to be concerned about unless it starts blocking off the water flow in your filter.

Filter media can clog with this muck over time and should be rinsed thoroughly every few weeks in a bucket of recent water change water, Not tap water.

Why Does My Fish Filter Keep Stopping?

A filter that continually stops flowing or running can be a real headache. The most common reason for this is a clogged motor that runs the impeller. If something is wrapped around the axle it could prevent the motor from running, and even burn it out.

Remove the impeller assembly and clean the motor axle thoroughly. Don’t use any chemicals to do this.

If the motor is clean but still won’t spin, then it’s probably burned out and the filter or motor itself needs replacing.

If the impeller is broken it may still be spinning, but unable to push the water through the filter media. This can be easily determined by removing the assembly and taking a look inside the intake.


Owner of AquariumGravel.com and also owner of actual Aquarium Gravel believe it or not! ;). Setting up beautiful aquarium sceneries and habitats since I was very young. Enjoy!