DIY Aquarium Filter from Pond or Fountain Pump

Homemade aquarium filter

In maintaining a 40 gallon aquarium, I find it maddening to have to keep buying filter packets for the standard aquarium filter that hangs on the back of the tank.

The filter pads need to be changed every couple of weeks and not only is this wasteful, but it is expensive.

To keep the tank clear, I find that one has to install a fresh filter packet at least once a month if not more often, and even on the aquarium page at Amazon, these costs can really add up.

Additionally, this is annoying because the entire filter unit has to be unplugged, carried to the sink dripping, and completely washed out because not only is the filter pack clogged, but so are the other internal parts.

Not only is this routine cleaning chore a messy hassle, but the biofilter inadvertently gets rinsed out as well (bad).

The biofilter is the black plastic sponge in which beneficial microbes are supposed to grow and live. It is this beneficial bacteria that keep the ammonia levels low for the health of the fish and also cut down on cloudy water.

The other annoying thing about the traditional filter system is that even after I clean it out and replace the filter pad, the system still does not do a very good job at filtering the tank.

I have always wished that I could build a better system to filter my tank.

Potential solutions to improving the filtration of an average sized home aquarium

In researching for this article, I came across the suggestion that I should an additional hang on the back filter (HOB filter); one for each side of the tank.  To me, that would just double the hassle of maintaining the tank, and would double the maintenance cost.

I’m sure the filtration of the tank would improve, and I do notice that professional tanks set up in dentist offices, libraries and the like often have a HOB filter on each side of the tank.

Other ideas involved building canister-type filters in which the water is actually pumped out of the tank, filtered in a separate container, and then pumped back into the tank; kind of like kidney dialysis.

For me, I get nervous with the idea of pumping water out of my tank and into another container in my living room! I know that attempting one of these systems could spell disaster in countless ways, in terms of leaks, overflow risks, etc. I want to be able to go on vacation and not worry that I may be coming back to a flood. Also, I feel like my 40 gallon tank is not big enough to warrant such an endeavor.

Other,more promising, DIY systems involved using a powerhead and some sort of a container filled with various filter medium. The container is submerged into the tank, and the power head sucks water through one end of the filter canister and pushes clean water out of the other end.

This submersible filtration system is what I am after, except I do not have a power head, which is a specialized aquarium pump that has one nozzle that sucks in water and another that pushes water out. Also, powerheads are nice but can be expensive, although the one I linked to is pretty cheap and high quality.


My solution was to tweak the submersible filter designs to incorporate the use of a small pond/fountain pump. I happen to have one of these, and even if I did not, they can be found for a pretty low price as can be seen in the link. A nice thing about using a pond/fountain pump is that they can also be used in aquaponics as well as in pond or fountain making, whereas a powerhead is only for aquarium water circulation.

Directions to build a submersible DIY aquarium filter using a pond or fountain pump:

Get a hard plastic container with a screw top lid. I used a whey protein container like this:

DIY Aquarium filter canister

The next step is to drill small holes in the lid, like this:

DIY Aquarium filter lid with holes drilled

The next step is to cut a hole near the bottom of the container for the nozzle of your fountain pump to fit into. I used a nail to punch a hole in the filter canister and then a knife to make the hole big enough to push the pump into, as shown below.

A hole saw kit for a drill would have come in handy but at the time I did not have one with a small enough bit.

Homemade aquarium filter

There is no need to seal the connection between the pump and canister as long as it fits snugly and will not come out during use. You could seal it with silicone, but I like it not to be sealed so that I can easily remove the pump when I want to clean out the canister. You can also clean out the inside of the pump (fountain/pond pumps have a removable casing).

That’s it!  Now all you have to do is fill the container up with a filter medium. For this, I used 100% polyester fiberfill (aka pillow stuffing). You can get a big bag of this for about $5 at a big box store or craft store.  The $6 bag I purchased is enough to last me five years.

Line the bottom few inches of the container with rinsed gravel or small rocks from your yard, and stuff the fiberfill in next. The gravel helps to weigh the container down; otherwise it will float.

Note on Filter medium

Check out the aquarium page on Amazon (link above) to find a whole host of various filter medium. Some people have suggested adding in activated carbon, which would provide even more filtering capability than using just the fiber fill and gravel. There are all kinds of other fascinating filter media that can be purchased and used in the submersible filter canister. I like to use stuff that can be washed and reused.

Place the filter into the tank and turn on the pump

I have found that placing the completed filter canister and pump on an elevated surface works the best. Position it on top of rocks, a brick, or whatever works best in your tank.

The Result

I can say that the filter works wonderfully. In 20 minutes, my tank was clear. The water is getting much more circulation as well, which is good for the tank environment. The pump does not make any noise (or at least much less than the old store bought filter did).

UPDATE: After a year of use, the filter system has worked beautifully. When the flow of water starts to slow down, as it ultimately will because the filter medium is collecting waste and doing its job, remove the canister and rinse out all of the components and you are back in business.

The only thing that I modified was the lid. I screwed the lid on and then secured it with 4 small wood screws because the lid had a tendency to pop off while in use. The screws can be easily removed for cleaning and then put back in to the same holes.

How it works:  The fountain pump sucks debris-filled water right through its intake openings and pushes it into the canister. The water has nowhere to go but up through the fiberfill ( or filter medium of your choice) and out through the holes in the lid.

The flow rate can be controlled by the regulator knob on the pump. But make sure that you buy a pump that is suitable for the size tank that you have (bigger is not better in this case).

The nice thing about this little system is that when the tank starts to look dirty, just remove the canister, open the lid, and wash out the fiber fill (maybe rinse the gravel too).

I am cleaning this new filter out a lot less frequently because there is about ten times the amount of filter media in the canister than what was in my hang on the back filter. So not only is this system sustainable and cheap, but it is also way more powerful and effective.

There is something quite satisfying about cleaning this filter set-up because you see all of the waste that was filtered out and you also have the satisfaction of knowing that you are reusing materials and saving money.

I plan to leave my hang on the back filter in place and designate it as strictly a biofilter. Since the water is being cleaned by my new filter, I should never have to clean out my hang on the back filter (or at least very rarely), so the beneficial microbes can be left undisturbed.  And I definitely won’t be buying any more expensive and wasteful filter pads!

UPDATE: After a few months, my store bought HOB filter that I was using just as a bio filter burned out, and I tossed it into the trash for good. For a bio filter, I added a cut-up sponge and some gravel into a small plastic bottle with holes punched into it. I ran the air hose into the bottle opening and turned it on. I let the bottle sink to the bottom of the tank. The air pump sends the air through the opening of the bottle, through the gravel and sponge, and out through the holes in the bottle. This is where the beneficial microbes live now.

Water changes

Another thing that really helps the quality of the aquarium water is frequently changing out some of the water and adding new water. Here is how we do this using siphoning:

  • Get a section of small hose about 3-4 feet long. Air hose works well for this, as does the size of hose that fits onto a standard pond pump.
  • Fill the hose with water, plugging each end with your thumbs
  • Place one end of the hose into the tank and the other into a bucket. The end that is in the bucket should be lower than the end that is in the tank.
  • Release your thumb and the water will siphon into the bucket.
  • Once the bucket is filled dump the water into your garden or use it to water house plants. Or you can purchase a siphon specifically designed for this use.
  • Replace the water siphoned out of the tank with water from your rain barrel (build one here). If you do not have rain water, use tap water that has been left out for a day so that the chlorine ha time to evaporate out of it.

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14 thoughts on “DIY Aquarium Filter from Pond or Fountain Pump

  • Patricia

    I’m new to this, but I’ve seen videos of ploepe cultivating plants that grow downward. I think for aquaponics, you can have various types of grow media such as gravel, river rocks, or clay hydrotons. I imagine carrots and such can grow downward in that. As long as the container is deep enough, perhaps it won’t restrict the growth and maybe it’ll work! As for the fish, it depends on the species, but I think it takes earliest 4-5 months from baby to edible age. Don’t quote me on that though.

    • Jonathan Davis Post author

      Yes you can, Patricia and I have done this with success! It is better if you can pump the water into a growing container above the tank that is filled with gravel or clay balls (hydroton) and then let it drip back into the tank. You have to be careful with the pump though to make sure you have an overflow safety in case the growing container gets clogged so you don’t have a flood, but there are ways to do this. But as you said, you can just let the plants’ roots grow directly into the tank (no pump involved). With this the problem is that not every plant likes to have roots that wet, but some do. Other issues I have run into are that you need to make sure your fish aren’t the kind that eat the roots (my cichlids that I have right now won’t let a plant of any kind grow for 1 day without devouring them! Another issue is light for the plants. Usually the top of aquariums are not near a direct light source, so you have to use daylight compact fluorescent bulbs to get enough lumens to the plant. A couple of CFLs set to a timer with 12 hours on and twelve hours off works well. Set the timer to less light if you want the plant to flower, simulating the end of the growing season.

  • Don

    I would recommend getting a biobag and filling it with activated carbon and AmmoLoc. Place this between the stone and fiber fill layer. The bag is reusable, and aquarium charcoal is very cheap. Activated carbon is necessary for removing most dissolved organic compounds, and the AmmoLoc takes care of ammonia.

    • Jonathan Davis Post author

      Yes, That would be even better, Don. I have gotten by OK without it but your addition of the carbon and AmmoLoc would definitely be an improvement. I grow a lot of plants indoors and out and frequently use the water in the aquarium to water the plants. I refill the tank with rain water from my rain barrel, which may be why my ammonia levels are not an issue (water is getting changed out regularly).

  • Jessica

    I was thinking of doing something very similar with a fountain pump I happen to have, but was worried that the pump may get clogged from the dirty tank water. Has this been an issue for you at all? And if so, what do you think a good solution would be?

    • Jonathan Davis Post author

      No, mine never gets clogged. The dirty water goes through the relatively large slots in the pump and into the filter canister. The inside of the pump does get dirty over time and when you clean out the filter canister periodically, you should remove the pump casing and wash out the inside of the pump. In fact, the slots in my pump are big enough to suck a small piece of gravel into it, and I guess that could clog it, but I have set it up so that the pump is off of the bottom of the tank about 3 inches and have had no issues. Thanks for the comment, Jessica!

  • John

    Love this! What GPH and brand of pump are you using? Is it the EcoPlus 396GPH your link goes to? Also is your tank the standard 40G or a 40G Long? Anything you would do differently? Taller/narrow plastic bottle? Clear bottle instead of black protein container? More holes/fewer holes? Also, does the pump discharge “push” a path through the fiberfill, or does it look like it is working it evenly?

    • Jonathan Davis Post author

      The pump I am using is slightly different–it is a 300 GPH, but the one I have linked to is close and would certainly work. My tank is a weird size, and perhaps more like 38 gallons–the tank dimensions are 30 inches wide by 12 inches deep by 2 feet tall. The container I’m using is 8 inches tall and the base is 5 inches in diameter. The pump pushes the water through evenly and does not force a path through the fiber fill. I have the bottom 2 or 3 inches of the container filled with gravel and then the fiberfill on top. The gravel helps to weigh down the container and may help to make the water flow more evenly. As far as what I would do differently, really nothing. The key is to get a container and pump that fit your tank. The size I have works for my tank and would probably work for larger tanks as well. For short and small tanks, obviously you would have to use a smaller container and dial your pump speed down. Remember, that these pumps are adjustable. The GPH rating is the maximum, but they can be dialed down. As to the amount of holes, I started with less holes and then ended up punching more holes until I achieved the flow that I was looking for. You can tinker with the pump dial and the amount of holes until it is working the way you want. Honestly, the measurements are not that critical, have fun! Oh, and as to the container, I used what I had around the house. Pretty much anything will probably work as long as it is pretty strong and has a secure lid. Clear might be cool so you could see it working. I originally used a small tote-like rubbermaid sort of container, but the lid was not strong enough and kept popping off. That is why I switched to the container in the pictures. Thanks for the comment 🙂

  • John

    I found an adjustable 400GPH (CHJ-1500) on eBay for $16. I couldn’t figure out why the pumps I was looking at looked so different than your picture, but then I figured it out: you put the pumps sideways so the discharge goes out on the right or left rather than the top. Then you just poke a hole in the side of your bottle near the bottom, put the pump discharge in the hole, fill the bottle with small rocks (for weight and distributing the flow) and polyfill, poke little holes in the bottle lid, screw it on, and you’re done. Perqs of this method: cheap, no proprietary filters needed, you can use whatever media you want (polyfill, Purigen bags, charcoal, etc.), always has priming water if power goes out, no waterfall noise like HOBs do, super easy to clean, and with a clear bottle, you can tell how dirty your filter media is, etc. Brilliant! And then your “bio-bottle” is another cool idea.

    1) You ziptied or bungeed your pump to the bottle, right, so it is more secure in the hole? Can’t tell from the picture.
    2) Still looking for a good clear bottle with a good lid and thicker plastic and round. Sam’s mixed nuts would work perfect, but it is square-ish.
    3) Have any problems with your fish getting too close to the pump suction?
    4) Do you have a separate air pump just for your bio-bottle? I’m wondering if just something simpler (a kid’s vitamin bottle with holes poked all over it, a sponge, and no air). (The filter bottle does all the filtering, and the bio-bottle you don’t touch, hide in the background, and just let it do it’s bio thing.)?

    I really appreciate your post and answers. I’ve been looking to do something like this for a while, and this is the head start I needed. Thanks!

    • Jonathan Davis Post author

      Your summary of the setup is spot on. To connect the pump, I made a hole in the bottle that is pretty snug so that just inserting the pump into the hole is good enough to keep it connected, but for good measure, I wrapped the cord around the bottle a few times and put a twist tie around it. I want to have something I can easily disconnect and reconnect for cleaning purposes. As far as clear, it might be cool, but on the other hand, it might be ugly to look at (fish poop). It’s up yo you. I don’t think the shape probably matters too much (round vs square). As far as suction concerns, I don’t have the flow so hard that it disrupts the fish at all. You want a nice slow flow that works over time. Just a little circulation is perfect. For the little bio bottle, I put the air hose into it to (1) keep the air hose at the bottom of the tank and (2) to provide a little circulation through the bio bottle. I would definately not use a second pump, and the air hose may not be necessary either, but I like it that way. Good luck, and be sure to send us an update. Thanks for your support. Once you have this mastered, another cool thing to try is our micro aquaponics setup.

  • Jane

    Very nice DIY instructions. couple of corrections though.
    1) though the instructions say so, you actually do not need to replace HOB pads every month. This is misleading instructions from the manufacturers in order to get you to spend more money. When it clogs (or your polyester fiber) all you need to do is rinse it in OLD tank water (that is important) to dislodge solids. Most of your biofilter (benefical bacteria) is in the filter and replacing it or rinsing it kills it with tap water can cause ammonia hikes that will weaken or kill your fish.
    2) when you rinse ANYTHING from your aquarium it must be in old tank water not straight tap water (or if not then tap water conditioned to remove the chlorine) Straight tap water will again kill the beneficial bacteria.
    3) most municipalities now use chloramine (that does not evaporate on sitting) rather than chlorine to disinfect tap water so if you are using tap water in your aquarium you HAVE to use a dechlorinator/water purifier. Water set out for 24 hours is NOT safe for fish. Rain water is–expect if you live in a crowded city in which case it MAY contain toxins from car exhaust or roof runoff.