Why Does Your Fish Tank Filter Keep Clogging (How to Fix it)

By Eddie Waithaka @aquariawise

How to Fix A Clogged Fish Tank Filter

The filter in your fish tank is clogging more and more frequently. You’re not sure why and you’re not sure what to do about it.


While there are many reasons for a fish tank filter to keep clogging, the most probable cause is that your filter is too small for the tank you have or the unit and filter media are not suited for the fish or livestock in your aquarium.

To keep your filter from clogging as frequently, replace it with one rated for double your fish tank size or add a second filter to relieve the load on the first filter.

With that brief introduction done, in this blog post, we’re going to explore all possible reasons your filter is clogging and what you can do to prevent it.

See the rest of the article below.

Why Does My Fish Tank Filter Clog So Fast

As noted in the introduction above, there may be several reasons your fish tank filter clogs so fast. Most have to do with your filter capacity vis-a-vis your fish tank size and stock.

In a nut shell,

Your fish tank filter clogs too fast because:

1.The filter is too small for your tank

2.Your tank is overstocked

3.Your fish has a high bioload

4.The type of filter you have

5.You are overfeeding your fish

6.Too much algae and plant debris in your fish tank

But for better insight, let’s isolate each scenario and take a clear look into what you might be dealing with.

Your Filter is Not Big Enough for The Tank Size

One possible reason your fish tank filter clogs fast is that the filter is not big enough for your tank size. If the filter can’t clean water in your fish tank enough times every hour, it is perhaps too small for your aquarium and will clog as frequently as every two days.

I recommend a fish tank filter that can turn over your aquarium volume four times per hour in an appropriately stocked tank with fish with a small to medium bioload.

For instance, if you have a 30-gallon fish tank, the recommended flow rate for adequate filtration would be 120 gallons per hour.

If you have an overstocked fish tank, add a filter that can turn over your aquarium volume 6 to 7 times in an hour and up to 10 times an hour in overstocked, with a heavy bioload stock.

You may even need a filter with more than 10 times an hour flow rate if you have something like a turtle in your fish tank.

Your Fish Tank is Overstocked

Overstocking your fish tank means more fish waste and leftover food for your filter to clean, which may cause it to clog frequently, especially if you’re not aware there is excess stock and fail to add a big or second tank filter.

To avoid overstocking your tank and stressing your filter, research any fish you want to add to your aquarium, considerating the stock you already have in the tank.

You also want to keep in mind the bio load of each fish because your stocking might be ok, but the waste your fish produce still overpowers your filter.

Only overstock your fish tank temporarily and with the intention to transfer some of the fish to another tank soon.

Your Fish Has A High Bioload (Produce Excess Waste)

Another possible reason why your fish tank filter clogs fast is your fish bioload. When you have species like goldfish and plecos that produce a lot of waste, purchase a powerful filter, preferably two or three times your fish tank rating.

You might also want to get an equally powerful filter if you have messy feeders, such as Oscars because too many leftovers will similarly clog your filter.

If you already have a good filter pump, you do not need to replace it. Purchase a second filter and run the two concurrently to reduce the workload on the one you had.


Bare in mind overstocking fish that produce plenty of waste or messy feeders will not only clog your filter. It will also mess up your water quality, result in ammonia spikes and even kill your fish.


Increase the frequency and size of your water changes to remove excess debris from your fish tank, which will otherwise clog your filter.

The Type of Fish Tank Filter You Have

You will find several fish tank filter types in the pet store, each made for different tank sizes and configurations. Ensure your is suitable for your aquarium, or add several filters for varying purposes to keep them from overworking and clogging.

Sponge filters are efficient in nano and mid-sized tanks, while HOB units and internal filters are suited for mid-sized and large, lightly stocked tanks.

Purchase a canister filter for any tank large than 40 gallons or when keeping fish with a high bioload.

It is best to have a canister filter even in small tanks unless it is a quarantine, breeding, or hospital tank. You can use a sponge filter for your breeder tanks.


Purchase a good and reputable filter brand, preferably those reviewed by other fish keepers, to save yourself the headache of cloggy, noisy, and all-around ineffective filters.

You May Be Overfeeding Your Fish

Overfeeding your fish causes two problems that clog your fish tank filter. Your fish will first feed more and produce more waste than usual. Then they will leave plenty of leftover food floating in the water or on the substrate for your aquarium filter to clean.

If you have an overstocked fish tank or fish with a high bio load, overfeeding your fish may even overwhelm the filter and make the water toxic to fish.

You will also note that some fish food causes a bigger mess in the fish tank than others and should be used sparingly.

You will want to feed your fish less homemade recipes, live foods, and slow-release vacation food (tablets).

That said,…

Offer your fish food one time a day in portions they can consume in three minutes or less. Remove any leftovers immediately and schedule a weekly cleaning, including a sand vacuum.

Cleaning your fish tank, vacuuming your substrate, and doing water changes two times a week is recommended if you have messy (wasteful) eaters or stock that poop a lot.

If your fish tank filter continues clogging even after you increase your cleaning and substrate vacuum, reduce the number of times you feed your fish in a week and add a second filter to your fish tank.

Whatever you do, be sure to avoid overfeeding your fish. A little food goes a long way, but excess fish feeds will only result in foul water quality and a stained filter.

Algae and Other Debris

Algae in your fish tank is another reason a fish tank will clog frequently. If the algae is sucked into the filter inlet with other debris, it may block the hose or the impeller.

To solve this problem, add algae eaters, reduce nutrients feeding the algae, reduce the light hours in your tank, and clean your fish tank frequently.

If the algae have already clogged the filter, you will need to clean it to get it working again.

How Do You Fix A Clogged Fish Tank Filter

There are a few ways to fix a clogged fish tank filter. The best way is to take the filter apart and clean it out. Remove any gunk in the impeller, hoses, and filter media because dirt mostly settles on the three components.

Do not rub the filter media because we do not want to kill the beneficial bacteria domiciled in the foam. Only rinse it lightly with some of the water from the fish tank.

You only want to remove the gunk and solid debris, such as algae, clogging the filter.

Use your hand or a light brush to dislodge clogs on the impeller. You can also use a small, hand-held Vacuum set on low to remove stubborn clogs from your filter.

If neither of the methods manages to dislodge the clog, you can try using a wire coat hanger or another suitable piece of wire. Bend the coat hanger into a hook to remove solid debris.

Remember to also check the intake and outflow hoses because they are prone to clogging, especially if you have algae in the fish tank.

Well, that’s all for this post.

I hope the post was helpful and we have answered your question sufficiently.

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