A fish pond biofilter made from an IBC tote

Building a Pond or Aquarium Biofilter

How To Build A Biofilter OR Life and Trophic Cascades

Ever wonder why maintaining a fish tank takes so much work while natural ponds, lakes, and streams require zero human intervention? One word – ecology. So let’s take a page from nature and establish a biofilter to maintain a clean, clear, biodiverse pond. But let’s first look at two ecological principles.

  1. Nature exploits unused resources, ie. Nature hates a vacuum.
  2. Life creates conditions conducive to life.

Let’s look at a pond’s natural cycling process to understand how these two principles apply to making a biofilter.

A fish pond biofilter made from an IBC tote
IBC Tote Biofilter Keeping a Pond Clean During A Pond Renovation

The Nitrogen Cycle

Fish Produce Ammonia

You decide to keep fish. Maybe you’re hungry; maybe you’re looking for companionship. Either way, you build a pond/aquarium, stock it with fish, and pick up some chow. You’re careful not to overfeed them, but every time you do, your fishy companions convert most of their food to ammonia-rich fish waste.

Ammonia Eating Bacteria Produce Nitrite

Unfortunately for fish, ammonia is highly toxic and, if left unchecked, will build up in the water and kill the fish. Ammonia displaces oxygen, causes organs to shut down, and makes fish susceptible to various diseases. Ammonia’s toxic effect is why it’s so effective as a household cleaner. Rub a little ammonia on a countertop; it’ll kill anything living there. It’s not the kind of stuff you’d like to swim around in.

If ammonia’s so terrible, why doesn’t it build up and kill everything? The answer is nitrifying bacteria. Some bacteria consume ammonia as food (nature exploits unused resources). These ammonia-eating bacteria are naturally occurring and will find your fish tank independently. However, you can speed up the process by adding nitrifying bacteria purchased at an aquarium store or stones and filter medium from a previously established fish tank.

Nitrite Eating Bacteria Produce Nitrate

Once ammonia-consuming bacteria establish themselves, ammonia levels will drop to zero. At this point, bacteria are consuming ammonia as fast as the fish can produce it. In a very real way, fish produce food for the bacteria (life creates conditions conducive to life). Unfortunately, our helpful ammonia-consuming bacteria convert that ammonia into a second toxic compound called nitrite. But just as before, a waste-consuming bacteria will discover this food-rich resource and sets up shop (nature exploits unused resources).

Sponges added to a biofilter to increase the surface area on which beneficial bacteria can grow.
Sponges are added to a biofilter to increase the surface area for beneficial bacteria to grow.

Plants Take Up Nitrate

After being consumed a second time, our toxic waste is converted to non-toxic nitrate. With ammonia and nitrite levels at zero, the fish can rest easy. But, if you’ve kept fish long enough, you’ve probably spent time removing algae from rocks and the walls of your tank. This is because nitrate makes an excellent plant fertilizer, and algae are essentially microscopic plants.

Like the nitrifying bacteria before it, algae set up shop to take advantage of this unused resource (nature exploits unused resources). We’re left scrubbing the tank and performing regular water changes to prevent algal buildup in aquariums, but it doesn’t have to be this way.

Bioribbon For Ammonia and Nitrite Consuming Bacteria To Colonize
Bioribbon For Ammonia and Nitrite Consuming Bacteria To Colonize

Plants Can Be Consumed

Algae are microscopic plants and almost guaranteed to search out and find your nitrate-rich fish tank – so why not intentionally include plants? Ornamental aquatic plants are an obvious choice, but there are other options. If your fish are herbaceous, you can grow food from fish waste – duckweed is a good option. You can add a grow bed (a biofilter with plants) to your tank and make a fish tank aquaponics system. If you encourage plants to live in your system, they will naturally remove the nitrate, so you won’t have to.

Here’s an article I wrote about aquaponics in schools.

Trophic Cascades

At each stage, a new organism was added to take advantage of the waste produced in the previous stage. A pond or an aquarium moves through a type of succession. Not only did each stage bring new life (nature exploits unused resources), but it also brought opportunities for new types of organisms (life creates conditions conducive to life). Fish and insects are keystone species in aquatic ecosystems that enable a host of other organisms to flourish. In ecological terms, we call this a trophic cascade. If you remove one component, the entire system will change.

Stepping away from fish for a moment, here’s a fantastic video from George Monbiot (4:34) on how wolves (and the trophic cascades they create) changed the ecology of Yellowstone National Park.

Building a Biofilter for Your Pond or Fish Tank

Fish Pond Biofilter From IBS Tote

To create an effective biofilter, you will need a lot of two things – surface area and water movement… and that’s pretty much it.

The nitrifying bacteria mentioned above form dense colonies growing on any surface that they can cling to. In the wild, this could be rocks, sticks, plants etc., though it could also be the surface of your fish tank, the pebbles at the bottom, plumbing, or a bunch of ribbon and sponges etc. In either case, the more surface area your pond has, the more beneficial bacteria your system can support. You can go to aquarium stores or online and buy materials such as bioballs or expanded clay pellets, but any non-toxic surface will do. I like kitchen sponges.

Water movement is essential to ensure that your bacteria comes in contact with the ammonia and nitrate it’ll be eating. Adding a pump to circulate water through a biofilter will ensure adequate contact. As a rule of thumb, I circulate the entire pond volume once an hour. Determine how much water your system holds, then pair it with a submersible pump capable of pushing that volume of water each hour.

Biofilter From An IBC Tote

In the system above, I filled a 275-gallon IBC tote with sponges and bio-ribbon purchased from an aquarium store to increase the surface area for bacteria.

I then ran two 1200-gallon-per-hour pumps from the pond into the bottom of the IBC tote biofilter. As the water level rises inside the tote, it contacts the bioribbon and sponges, eventually overflowing through a two-inch pipe at the top. Adding water to the bottom of the biofilter and overflowing from the top forced the water to move through the surface area medium inside the biofilter.


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