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How to Set Up an Undergravel Filter (for Easy Tank Cleaning)

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By Lindsey Stanton

Aquarium with undergravel filter

Don’t let anyone tell you undergravel filters can’t be an effective filtration option for your tank. When done right, they can be POWERHOUSES for stabilizing a healthy aquarium. The traditional undergravel filter setup method is straightforward, but there are some pretty major drawbacks to this setup (which is partly why they have fallen out of favor in recent years).

  1. Gunk gets trapped in the rocks and under the filter plate.  Not only is it hard to clean, but actually, this can be a very dangerous problem – especially if not cleaned very frequently. These pockets can become anoxic, and nasty disease-causing bacteria can form in these areas, leading to sick fish. Even if you vacuum out the gravel frequently, you still can have all this debris lodged under the actual plates that can’t come out without a deep cleaning – sometimes necessitating a tank tear-down.
  2. Small gravel poses a choking hazard for some fish like goldfish.  Bigger or adult goldfish especially are prone to getting “rockitis” where the gravel actually gets lodged in the back of their throats, blocking their ability to eat and causing other symptoms like lethargy and strange mouth movements.
  3. Difficult to grow plants in directly.  Plants can grow roots into the filter plates and restrict the water flow through the filter, destroying the effectiveness of your filtration.  If you want rooting plants it’s recommended to keep them in something like a glass plant jar.

I’m not saying never ever do it this way, or it’s the end of the world if you do. But I think there are some better ways that will make your life easier and keep the risks down for your fish.

My motto? Fishkeeping should be as simple as possible. So today, I’m going to share the top 2 ways to set up an undergravel filter that overcome both of these problems and make your biological filtration MUCH more efficient in the process!

How to Set Up a Safer, Easy to Clean Undergravel Filter for Your Fish Tank

I’m giving you the 2 best methods I know of. There may be others I haven’t tried that are just as good or even better. Also, don’t be afraid to get creative and experiment if you want.

For what it’s worth, I really like the Penn Plax line of undergravel filters as they can be customized to fit almost any dimension of tank.

penn plax undergravel filter

You can also piece together several smaller sizes if your aquarium has a unique footprint. Whatever works for you. You can use the setup designs below alone or in conjunction with another kind of filter.

The Sand Cap Method

This idea combines the benefits of sand (which does not trap muck like gravel) with the efficiency of undergravel filtration. I recommend using CaribSea aquarium sand, the Crystal River style.

Out of all the sands I’ve tried, this one works the best. Why? The grain size is much larger than average sand but still small enough to prevent fish from choking while having the debris sit on top, patiently waiting to be vacuumed.

One big advantage of this method is you don’t have to deal with plants rooting in the filter plates, which is a big problem for growing plants with traditional UG filter setups.  Due to the strategic placement of the polyfiber barrier, this method is ideal for keeping rooting plants.

I highly recommend adding some heavily rooting plants as it will keep the substrate aerated and help lock down the gravel-type media under the sand for those with digging fish.

Not all plants enjoy soil aeration, but some like Amazon Swords really do. The roots cannot get through the barrier and block the flow, but the water can. The barrier is not thick enough to serve as mechanical filtration, and even if it were, it is far down below the layers of sand and gravel-type media. This means it does not need to be replaced continually.

  • 1. Place your assembled undergravel filter plates on the clean, bare bottom of the aquarium. If your tank is already set up, it is a good idea to do a thorough vacuum and water change.  You will need an air pump and airline tubing to run the airstones in the filter. I use the double outlet airline pump as you don’t have to T off the airline tubing, and you only need to use 1 outlet to run it.
  • 2. Cut a piece of thin polyfiber padding to fit over the surface of the plates.  This will ensure no fine debris or sand can work their way down underneath the plate and get nasty over time.  I used an Imaginarium thick polyfiber pad torn into 3 thinner layers and spread them on the filter plates, snipping a slit in the fiber where the uplift tubes connect.  It’s ideal because the structure allows a lot of water flow while preventing sand and debris from entering.  You don’t want to use something that will break down over time, like a cotton cloth.
  • 3. Pour a 1/2-1″ layer of gravel, pre-soaked Seachem Matrix or crushed coral (for hardwater fish like cichlids) over the polyfiber.  This will help with water circulation as well as provide additional surface area for biological colonization.  If you use crushed coral or another porous substrate, you can also provide an area for denitrification (aka nitrate reduction) to occur, which would not happen with gravel.  On top of this layer (optional but not mandatory), you can place a layer of mesh or gravel tidy to prevent this layer from intermingling with the sand.
  • 4. Pour a 1.5-2″ layer of sand over the gravel.  If you have digging fish you will want to use about 2″ to prevent them from disturbing the gravel underneath.

Most UG filters come with little carbon inserts you can put on the tips of the uplift tubes. If you’re like me, you find this unsightly. Part of why I love undergravel filters is because they are just about invisible, and I don’t want distracting little black squares in the tank.

So, where do you add other kinds of media (maybe Phosguard, Purigen, Algone, active carbon, or otherwise?) With this particular setup, it isn’t really that easy as in to push aside all the stuff on top of the filter plates and bury your packets of chemical filtration as it would be with a regular undergravel filter setup.

And if you have plants rooting, forget about it. But there’s a workaround. I use this little internal power filter just big enough to put my chemical filtration in, stuck behind a rock and plants.  It doesn’t have to be huge, as it’s not functioning for biological filtration (you are more than covered on that!).

Yes, it gives you another black cord to deal with, but hopefully, your tank is planted enough that the stems and leaves can conceal it.

The Reverse Flow Method

Reversing the flow has some major advantages (source).

Here’s how to do it:

  • 1. Place your assembled undergravel filter plates on the clean, bare bottom of the aquarium.  No need for the airstones here.
  • 2. Pour a layer of gravel or larger porous filter media (such as Seachem Matrix, Pond Matrix which is a bit larger than Seachem Matrix, or Hydroton).  You can also use larger river pebbles, though these may restrict the water flow more and won’t support nitrate reduction.
  • 3. Use a submersible powerhead to force water down the uptake tubes.  This is what reverses the flow and pushes water up through the substrate rather than forcing waste down.  Pumping water through the substrate upwards keeps it free of mulm-buildup, which can cause deteriorating in water quality.
  • 4. Install a prefilter on your powerhead to prevent debris from being pushed by the powerhead underneath the filter plates.  This is really a must or you will end up having the same problem as a regular undergravel filter setup.

It’s a good idea to supplement this method with an airstone, sponge filter or HOB filter for aeration and surface movement. Connect it to a canister filter packed with mechanical filtration media to purify the water first before it sends the flow down the UG filter tubes from the outlet.

Hello, sparkling clean water!

goldfish gravel substrate
Image credit: Pixy

Advantages of Undergravel Filters


Annoyed by loud sputtering, gurgling, trickling, or dripping from other kinds of filters? The only noise just about will be coming from your air pump vibrating (if you use one). If you work in an office or want a quiet tank in your room, this can be a big perk.


Just about every filter out there is an ugly intrusion into your beautiful aquarium scene. There’s almost no way to hide most of them. With Undergravel filters, you integrate the filtration so closely into the aquatic environment there is almost no transition.

Huge biological footprint

You can’t beat the surface area the size of your aquarium’s footprint. End of story.

Substrate Aeration

It prevents bad anaerobic forming in the substrate when set up using the methods described above. It’s okay to go heavier on your layers of substrate since you are getting oxygenation happening.

fish divider


I hope this post sparked your interest in the possibilities of filtration with undergravel filters. What about you? Have you tried them, and what have been the results in your tank?

Featured Image Credit: PDPics, Pixabay

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