Part II: How to Build a Backyard Pond with DIY Biofilter

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Last year, we wrote a DIY backyard pond article that has become quite popular. We built the pond for our backyard ducks, but the concept could be used to build a backyard pond for anyone. In fact, it would be way easier to have a pond without a flock of ducks constantly in it, molting feathers and, er, using it as a giant toilet.

Our DIY backyard pond on a cold winter day.

Our DIY backyard pond on a cold winter day. You can get step-by-step instructions which include a detailed materials list here.

A recent commenter on that article, “smithmal,” asked some great follow-up questions about our backyard pond system. Rather than try to answer all of their questions in the comments, we decided to break out the answers into their own article. Thanks for your questions, smithmal!

Questions & Answers About Our Backyard DIY Pond System

1. How is your system working so far? If you were starting from scratch over again, is there anything that you would change?

After four and a half years (we built it in Jan 2014), our duck pond continues to work great — especially considering that there are 6 ducks sharing the same ~1,200 gallon pond with two fish. That’s a lot of poo to process. Hindsight changes?

  1. As our original article noted, we did decide to add a second filter pond + smaller pump + secondary waterfall to our original system to help filter out more of the biosolids and increase aeration.
  2. We also added ball valves to our filter pond plumbing so that the filter pond water didn’t suck back down into the main pond during cleaning when the pumps are turned off (more on that below).

Looking back, I don’t think we’d make any significant changes to our pond system beyond those two additions, given our space and budgetary constraints.

I largely have The Tyrant to thank for how well things turned out since she has a strong biology and research background, and she did the bulk of the mental lifting on this project. I’m more the brute labor who screams “meat” or “water” when I need to refuel.

Our girls love their backyard pond and spend hours swimming and playing in it each day. DIY backyard pond article - answers to questions

Our girls love their backyard pond and spend hours swimming and playing in it each day.

2. Can you provide a brief description of how you clean your biofilter bogs?

Have you ever seen the show Dirty Jobs? If cleaning our pond biofilters was a salaried position, we would definitely warrant a visit from Mike Rowe. Since we don’t pay ourselves for this activity, we’ve thankfully managed to avoid the fanfare and TV show fame. 🙂

As our original pond article details, you can use any number of things for a filter medium: sponges, steel wool pads, hog’s fur filters, etc. The filter medium serves two primary roles:

  1. To provide a place with lots of surface area for the de-nitrifying, water-cleaning bacteria to take up residence, and
  2. To capture the “muck” as it comes flowing through the system.

You’d never see as many ducks and fish continuously using the same small water source in nature as we have in our backyard pond. If we just had a couple fish, we’d probably never have to clean our filter media. But once you start adding ducks to the equation, that means regular, manual filter cleaning is something you’d need to plan for.

We’ve gotten in the practice of cleaning our filters ~quarterly. I should also note that we use this water quality test kit, and even when our water looks relatively gross (murky, brownish, greenish), it still tests really well, which has surprised us. To clean our pond biofilters, we do the following:

  1. Unplug our pumps to turn them off;
  2. Immediately turn the ball valves on our plumbing system so that the filter pond water does not suck back down into the main pond;
  3. Take all the sponge material out, put it in a wheel barrow, then rinse the sponges out and use the “muck water” on the perennial fruit & nut trees in our garden (we don’t recommend applying this water on any plants you’ll be directly eating anytime soon);
  4. Bucket or pump out the muck water in our empty pond filter before returning the filter material to the empty container;
  5. Turn the pumps back on and add a bit of water to the pond via a drinking safe hose to bring the water back up to level.

*While we have the pumps turned off, we quickly unclip them from their pipes, remove them from the pond, pop them open, and give them a good cleaning. It takes one person about 5 minutes to clean both pumps.

3. Do you get sediment forming at the bottom of your pond and if so, do you need to clean out your pond? I’m wondering whether a swirl pool between the pond and the skippy would remove large particles and reduce the bioload on your skippy filters?

The only time we get much buildup in the bottom of our pond is in the fall when the huge oak tree in our backyard drops half of its leaves into the pond. Unfortunately, that means that I have to hop in to the pond a couple times each year to pull the leaves out by hand or by net. Thankfully, the pond is only about thigh deep (I’m 6’1″). If it weren’t for the oak tree, I don’t think there’d be significant buildup of debris in the pond.

What about a swirl pool? We’re not aquaponics experts, so it might be worth someone else giving this a shot. I’m not sure how that would work though, given that our pumps are situated in the bottom of the main pool and they aren’t able to pump up large debris/particles.

4. In addition to your skippy (microbe) filter, have you thought about filtering your water through an hydroponic system? The plants you use could provide additional filtering and landscaping to your pond. Also, some of the plants you grow could be given back to your ducks as an additional source of nutrients.

Yes! We’d love to use the water from our pond to feed plants in a hydroponic system. Problem is every edible plant we put anywhere near the pond gets immediately eaten by a flock of feathered terror-birds, aka ducks. Also, we don’t have the space in our back yard or the inclination to set up an elaborate aquaponics structure, so we grow food with the water in a less technologically sophisticated way… As mentioned above, when we clean the filter ponds, we use that water in our garden.

They might look cute to you, but these vicious Welsh Harlequin ducks strike fear and terror into the heart of vegetable patches. DIY backyard pond article - answers to questions.

They might look cute to you, but these vicious Welsh Harlequin ducks strike fear and terror into the heart of vegetable patches.

We also have designated “duck gardens” where we grow plants that our ducks love – chickweed, chicory, lettuce, etc. We’ll use some of the pond filter water on those beds as well, to keep that virtuous cycle on repeat.

5. I see that you keep your pool open year round. What happens to your microbe population during the winter time? Do you need to re-populate it in the spring again?

My guess is that water microbes work similarly to soil microbes. Each season sees different species active, and the warm months are when the widest range of species are most active. Just because warm weather bacteria are dormant in the winter doesn’t mean they won’t perk right back up when water temps return to a favorable range though. Nevertheless, we have two factors working against us in our system as we try to “team” with our microbes:

  1. Significant pressure on our pond from duck and fish waste relative to the size of the pond and the number of beneficial microbes that can reside there;
  2. We clean our filter medium, so we’re likely getting rid of a significant portion of our microbes.

That means we do add beneficial microbes back to our pond a few times per year, usually after a cleaning.

  • Cool weather transition bacteria – to help break down pond debris in the late fall as we head into winter, we use this pond bacteria;
  • Winter pond bacteria – Throughout the winter, we’ll use this cold water pond bacteria;
  • Warm weather transition –  We use this pond bacteria in early spring (mid to late April in our Zone 7B) as soon as the pond starts to warm up;
  • Summer pond bacteria – during the warm months we use this warm water pond bacteria.

Do we have to use all of these pond bacterias to keep the system in balance? We don’t know but we don’t really want to risk it since our ducks’ health is at stake. We’d rather pay a little upfront to keep things in good order rather than pay for a sick duck later. It’s a bit like using a compost tea as a foliar spray in your garden to prevent pathogenic microorganisms from gaining a foothold – prevention/maintenance is always much easier and less costly than fixing a sick or broken biological system.

6. Can you explain where your pumps are placed. Are they both in the skippy filtering pools? How long do you think your pumps will last since they are dealing with pumping water with heavy bioloads in them?

This image shows the pump placements and filters they pump to (sorry the images appear small – you can click to enlarge).

backyard pond plans showing pump placement

Our pond setup showing the pumps (in the water), plumbing and respective filters that they pump to. (click the image to view a larger version)

  • Our large primary pond pump, the Laguna Max-Flo 2900, is situated at the lowest point in the center of the large end of the pool. We have it propped up off the bottom of the pool on top of a large flat rock to reduce the likelihood of it getting clogged with leaves/debris.
  • Our smaller secondary pond pump, the Laguna Max-Flo 900 which we added when we put in our second filter pond, is on the opposite side of the main pond (the small side). Each pump is plumbed to pump water out from the bottom of the pond, up and into the BOTTOM of its designated filter pond. Then the water filters up through the filter media in the bog and out of the top of the bog pond down a waterfall and back into the main pool.

7. Would you consider shooting a video of your pond system and narrating each section of your pool. A video would help out a lot with visualizing how your pool and biofilters work together.

Sure! We’re not great at video editing and have severe time constraints right now since we’re also starting a farm, but we’ll try to get some pond videos posted over the next quarter. Hope this helps and let us know if you have more questions. Same goes for anyone else with new questions!

More Questions?

Shoot – we’re here to help! Add them to the comments section below.

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  • Reply
    May 3, 2021 at 12:12 pm

    Do you ever have problems with algae in your pond? We just built our pond modeled after yours and used the bacteria you recommended. It’s been a few weeks and after a few hot, sunny days, the pond is green with algae. I don’t know if the bacteria haven’t had enough time to take care of the problem or if we need to add other things to get rid of the algae?

    • Reply
      Aaron von Frank
      May 4, 2021 at 7:44 am

      Hi Nicole! It would be really strange for water straight from the tap to already have an algae bloom. That usually requires a good bit of nitrogen and/or other nutrient buildup. We just did our “annual” cleaning on our pond yesterday where we completely clean out the filter ponds, filter pads, clean leaves and debris off the bottom, and do a water changeout. I put “annual” in quotations because we actually haven’t done it in two years due to having a baby last year and just not having any time to spare. Our pond water was starting to have an algae bloom and the water was turning green with the nutrient buildup and onset of hot weather (it’s in the 80s here now).

      How many ducks do you have in your pond? Regardless, it’s possible that either:
      a) the chemical compounds in your municipal water killed the bacteria you put in your pond, or
      b) the bacteria just hasn’t had time to fully establish and start working.

      The bacteria kicking in is not an instant thing; it seems like it takes a week or so before you start seeing a noticeable difference in water quality. Recommendation: wait another week and if your pond water hasn’t started to clear up, add another round of pond bacteria. By that point, the bacteria-killing compounds in the municipal water will have long since dissipated or degraded, and you’ll have given the first round of bacteria ample time to start working. So whether it’s problem a or b, you’ll have your bases covered.

      Hope this helps and please check back in to let us know how things turn out!

  • Reply
    April 10, 2021 at 7:24 am

    Hello, thank you so much for sharing this information. I plan to follow these instructions to build a pond for my 3 ducks this summer. Do you think a 100 gallon bio filter would accomplish what your 2 50 gallon filters do? We don’t have the space for 2 bio filters. Thank you!

    • Reply
      Aaron von Frank
      April 10, 2021 at 9:10 am

      Hi Melissa! Yes, you should be fine with a total of 100 gallons of filter pond. Actually, you should be more than fine given that you’ll only have 3 ducks using the pond, but it’s always better to have more capacity than you need because you never know how many ducks you’ll have in the future. Best of luck with your pond and let us know if you have questions as you get going!

  • Reply
    Edward Blank
    March 24, 2021 at 4:12 pm

    Thank you for your detailed instructions…could you tell me how many layers of the Filter media/pads: Matala Filter Media Pads – (Green) and Matala Filter Media Pads – (Grey). did you use?

    Pastor Ed

    • Reply
      Aaron von Frank
      March 24, 2021 at 5:27 pm

      Hi Ed! Not sure the exact number of layers but we only used two total pads (they’re large). We started by cutting out a form from each color (green and grey) that fit snuggly into our filter pond – so two deep there. The remaining pad material was then cut into smaller pieces, which were stacked. Guesstimate is that the total combined thickness of layers is somewhere in the ~8-12″ range.

  • Reply
    Brian LeDonne
    January 16, 2021 at 9:14 am

    Question – when the water rises in the pond bog filter and looks like it pours out/over and creates the waterfall…Can you please explain how the water is directed down the waterfall into the main pond?

    • Reply
      Aaron von Frank
      January 16, 2021 at 12:02 pm

      Hi Brian! We cut a rectangular section out of the filter pond lip, and use use pond glue + piece of pond liner to created an overhang so the water pours out of the filter pond and over the rock below it, which is where the waterfall begins. Please let us know if you have any other questions, and best of luck!

  • Reply
    November 12, 2020 at 2:11 pm

    I have a flock of 16 ducks, so almost 3x your flock size. Does that mean I need to triple my pond in order to keep the ecosystem & biofilters working properly?

    I need to build something quickly because although I have a couple kiddie pools (which they enjoy), the ducks inevitably end up in my person swimming pool, which is about to cause a divorce. LOL. (Note: we also have a 1 acre fish pond, about 1000 feet away, but the ducks are scared of it) Thanks for your help!

    • Reply
      Aaron von Frank
      November 13, 2020 at 11:18 am

      Hi Melissa! You’ll probably be fine building a 2x larger pond, but if you have the space and resources, it certainly can’t hurt to go larger. Funny that your ducks are afraid of your actual pond! We once brought our beloved pet duck, Svetlana, to the family lake house and she was absolutely terrified of the giant lake. Perhaps it was the size and all the other wildlife present. Maybe that’s how a hunter-gather human would react if you dropped them in the middle of New York City. Who’s to know the mind of a duck. One thing to be mindful of is the potential for snapping turtles to come out of your real pond and take up residence in your artificial pond. Even though we have a 6′ fence all around our backyard, a small snapper somehow got in and decided our duck pond would be its new home. Our ducks stopped using the pond for a few days and would stand next to it looking in and honking – that’s the only way we knew there was a snapping turtle there since it blended in so well. We caught the bugger in a net and re-homed it a few miles away in a swamp. Anyway, good luck mending your marriage while accommodating the needs of your ducks. 😛

  • Reply
    September 27, 2020 at 10:23 pm

    Hi! My husband and I rescued a duck with a broken leg and a friend for him then due to the touch and go situation got two more friends just in case. Thank God for your site! Also thank you 🙂 question, we just built a pond but since we live in NE Ohio we will be getting lots of snow and below freezing days. How do you keep your pond from freezing? Thanks!!

    • Reply
      Aaron von Frank
      September 29, 2020 at 3:20 pm

      Hi Julie! Sounds like you’ve taken on quite a project! Ducks + pond in NE Ohio. We’re in a temperate/mild climate region down here in Upstate South Carolina. The coldest temps we ever get are single digits, but we do get frequent sub-freezing day and night temps throughout the cold months. We keep our pond from icing over two ways:
      1) Moving water – Water running through the pipes will not freeze unless it gets REALLY cold. Our pipes didn’t freeze when it hit 5F. We have two waterfalls in our system, and that also helps keep the water surface from freezing.
      2) Mentioned in our “how to build a pond” article, but we have a pond de-icer we use during cold spells that does the rest of the work for us. Here’s the Amazon link in case that’s something you want to get: The de-icer might not be effective at keeping the surface ice-free in your cold climate, but it will at least keep an opening in the ice to allow gasses to escape the water which will preserve water quality throughout the winter.

      There may be some sort of pond heater you could get but we’d be stepping outside of our knowledge/experience zone in recommending anything in that department. Regardless, best of luck to you and your new duck family!

  • Reply
    Linda Weaving
    August 4, 2020 at 8:59 pm

    Have you considered a reed bed system and could such a system work instead of or in addition to the skippy pond? My garden is very ornamental and I wouldn’t want to have the pipes visible. I also plan for a 1metre waterfall, so would that do the job of your two waterfalls? Could the pond size be scaled down? What would be the volume you’d recommend for a couple of miniature ducks?

    • Reply
      Aaron von Frank
      August 11, 2020 at 3:41 pm

      Hi Linda! Responses to your questions:

      1. You could use a reed bed system, but a) it would likely require a lot more room than a skippy biofilter system, and b) you’d have to fence it off or somehow keep your ducks out. Ducks will eat or destroy pretty much any plant you put in the water with them. The only plant we’ve managed to grow in the pond with our ducks is a marsh iris inside a pot with rocks to keep them from pulling out the bulbs.

      2. You could very easily cover/obscure your pipes with rocks, pond liner, plants, etc. We didn’t do a great job with that.

      3. The waterfalls are more for aerating/oxygenating the water than cleaning, although they do do a bit of cleaning. A 1 meter waterfall should be fine and you could scale down the overall size of the pond and still be fine there as well. There’s no hard-and-fast rule on square feet of pond per duck, but we’d recommend going as large as you’re able. Two miniature ducks don’t need a huge pond (you could do half our size or smaller), but they’ll be happier with more water and the water quality will be easier to maintain. Hope this helps!

  • Reply
    January 17, 2019 at 2:44 pm

    Just wondering if there’s a reason you have the 2nd filter fall into the first? Or can I just put the 2nd filter in a different area and make my 2nd waterfall that way.
    Thanks for all this. I can’t wait just getting started.

  • Reply
    Rodrigo Pellegrini
    January 17, 2019 at 2:44 pm

    This is amazing, i’m a duck evangelist as well and i will follow your guidance and try to build a pond myself.

  • Reply
    April 24, 2018 at 12:53 am

    Wow!!! Thank you very much for answering all of my questions so thoroughly. I really appreciate it. Glad to hear that your system has been up and running for three years. I think that is a good enough time period to be able to provide a realistic review of your system. Most videos/blogs I’ve seen/read provide feedback right after a pond has been built rather than waiting/returning after a couple seasons which I think provide a much more realistic overview of a working system.

    I’m definitely interested in putting in a system like this. The only thing that I’m still exploring is whether to use a submersible pump or an external pump. I’m thinking about maybe using an external pump as it would be easier to access for cleaning and provide a longer working life since as it would have to deal with pumping water with as much biomass since the water could be pre-filtered before entering the pump. They are however more expensive.

    Thanks for listing all the microbes you use with your skippy filter. I’m a little confused about when and how you introduce each variety of bacteria to your biofilter. Could you expand on this?

    In terms of pumping out the water in your biofilters, have you thought about building a drum reservior with a spigot and attaching a dry vac to it? I use this type of system for collecting the rinse when cleaning duck sand and then adding the rinse to my fruit trees. I think it would work great in your system as well (see vid here:

    Whenever you get the time, a video of your system providing an design overview and maintenance would be much appreciated.

    Thanks again!

    smithmal .

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