How To Cycle Aquaponics Systems

Before adding fish or plants to the system, you need to establish the Nitrogen Cycle.

Once you have a system fully built you need to go through the process of cycling your aquaponics systems before you start growing. Cycling is key to establishing the synergistic relationship with the fish and the plants. Cycling is where you’ll establish your colony of beneficial bacteria that play the critical role of converting the ammonia from the fish into a usable form of nitrogen for the plants via the nitrogen cycle.

Without properly cycling the system we would be feeding our plants ammonia, which they can’t use, and so it wouldn’t get removed from the system and would simply build up until both the fish and plants died. Obviously, we want to avoid that and instead create conditions for both to thrive. That’s where cycling comes into play.

What is Cycling?

Cycling is the industry shorthand for establishing your nitrogen cycle and building up your populations of nitrifying bacteria. The nitrogen cycle again is the process that consumes ammonia, and produces nitrites and then consumes nitrites to produce nitrates which our plants use as food.

You initiate cycling by adding ammonia to your system. This can come in the form of concentrated ammonia products or naturally by adding fish and waiting for them to produce ammonia. The presence of ammonia will naturally attract Nitrosomonas, the first team or nitrifying bacteria, to your system. You can speed up the process by adding concentrated nitrifying bacteria readily available from an aquarium strore. With the addition of Nitrosomanas, we will see our ammonia levels start to fall and our nitrite levels start to rise. The presence of nitrite will then attract our second team of beneficial nitrifying bacteria, Nitrobacter, which will consume our nitrites and produce nitrates. As a result, we will see our nitrite levels fall and our nitrates will begin to rise. Eventually, you will hit an equilibrium where e

From there the cycle gets interrupted as the plants take up the nitrates, cleaning the water for the fish, and the water gets sent to the aquaculture tank(s) to get populated with ammonia waste from the fish and start the cycle over again.

You’ll want to be testing your water at least weekly and ideally daily during the cycling period so you can observe these changes, do a water exchange if the ammonia or nitrites ever get too high, and know when it’s safe to add your plants, and depending on the method, your fish.

Cycling Aquaponics Systems With Fish

Using your fish is the most common way to cycle an aquaponics system, especially at the non-commercial level. It requires almost no effort outside of patience. Some view it as easier than the other methods because you don’t need any extra inputs, others view it as more stressful because you likely have a bunch of fingerlings that are not as hardy as full grown fish and could die during the cycling process. That’s why close monitoring of your levels is important to keep your water within hospitable levels of ammonia and nitrite for the fish.

If cycling with fish, it’s important not to stock to your full stocking density right off the bat. Your challenge will be to get the system cycled fast enough that the ammonia concentration drops to non-toxic levels before it affects the health of the fish. We recommend stocking at half density until your cycle is fully established with plants in the system. During this time don’t feed your fish more than once a day and feed them at a reduced rate. Make sure to observe the feedings and remove any food not consumed within 5 minutes.

During cycling, a general rule of thumb should be to keep your ammonia and nitrite levels at or below .50 ppm (parts per million. An API Freshwater Test Kit is the easiest way to monitor your levels and can be purchased at any pet or aquarium store or online here. Thi cycling with fish method takes about 30 days naturally but can be quickened to as few as 7 with the addition of concentrations of nitrifying bacteria.

Cycling Aquaponics Systems Without Fish

Another way to cycle is not to use the fish to provide ammonia but to simply dose your system with ammonia prior to adding fish and plants. There are several ways to add ammonia, we’ll cover the most common.

Liquid Ammonia: Only use liquid ammonia if you can find it in the pure form that is made strictly out of water and ammonia (usually 5-10% by weight). Avoid anything with perfumes, colorants, soaps, surfactants or any other additives. If it foams when you shake it leave it on the shelf. If it doesn’t list it’s ingredients leave it on the shelf. Hardware stores or cleaning supply stores usually carry it. It can also be found online here.

Ammonium Chloride – Crystalized ammonia is another form of pure ammonia that may be little easier to find locally as it is available at aquarium supply stores, soap supply stores, photography supply stores and chemical supply stores. It’s more expensive than pure ammonia, and you want to try and find a kind that’s intended for use in aquariums as you can be sure that won’t have any additives.

Instructions for Fishless Cycling
  • add ammonia to the tank a little at a time until you get a reading from your ammonia test that reads 2ppm. Keep track of how much you add each time and record what it took to get to 2ppm.
  • Add your recorded amount daily until you get nitrite levels of .5ppm. If your ammonia levels ever get above 4ppm, stop adding daily until the levels fall back below 4ppm.
  • Once nitrites appear to cut back on the daily ammonia dose to half of the original volume. If nitrite levels exceed 5ppm stop adding ammonia until they decline until 2ppm.
  • Once nitrates appear (5-10ppm), and both ammonia and nitrite levels are showing 0, you can stop adding ammonia.
  • Wait a day just to be sure and then you can add your fish to your system.

You can add plants at any time throughout this process as they do have some ability to take up nitrogen from each stage of the nitrogen cycle. However, they will be happiest and show the best growth when the cycle is fully established.

Cycling Aquaponics Systems With Seaweed Extract

This is a technique we learned from Murray Hallam, a prolific aquaponics systems designer, and consultant out of Austrailia. He’s one of the originals in the industry and has been teaching others how to successfully do aquaponics at any scale for over a decade. He’s used this technique on hundreds of systems.

Instructions for Seaweed Cycling

  • Add liquid seaweed extract, such as Maxicrop, to your system using 1 quart for every 250 gallons of tank water in your system. (Fair warning it will turn your water black, but it clears up in a weeks time)
  • Add plants after adding seaweed extract
  • Wait two weeks
  • Add fish (preferably at a low stocking density for the first few weeks time)

This is a great option for people who can’t get synthetic ammonia in their area. The liquid seaweed has a small amount of ammonia that will begin the cycling process, easing the ammonia load on the fish so that by the time they get in the system they won’t be stressed by high ammonia levels.

How To Speed Up The Cycling Process (good for any of the above methods)

As I eluded to earlier you can speed up the natural cycling process which takes about thirty days and shorten to as few as 7 days. Adding nitrifying bacteria, whether from an existing aquarium, commercial product, or if you are lucky an established aquaponics system is the best way to jumpstart your cycling process.

Adding Bacteria

There are basically two ways to do this, adding media or bacteria from an established aquarium, lake/pond or established aquaponics system or adding bacteria from a commercial product of nitrifying bacteria. If you are adding from a non-commercialized source, remember that bacteria require a biological surface area in order to reproduce. So you want to either take some surface area from the source, or soak something with surface area in your source to make sure you are bringing a good population of bacteria into your system.

Good Bacteria Sources

  • Media from an established, healthy and thriving aquaponics system. Media from a media bed or biofilter would work best. You can also soak new media from your system in an established system for a few days and get a nice colony of bacteria that way as well.
  • Filter material/media from a healthy, disease free aquarium. So for example, if you have an aquarium filter with replaceable filter material, you can throw that filter material into your system.
  • After that, rocks from a backyard pond with fish in it. I would say this is the last resort option as it will be hard to determine if the pond is disease free. You could also go to a fish store and ask them for some filter media or gravel from their tanks to bring to your system. I would only do this at a local independent fish store and not places like Petco or Petsmart as they regularly carry fish with disease simply from their volume. A local store would likely be more honest and could steer you to tanks with disease free fish you could grab some media from. If they won’t give you a filter media, ask them to squeeze it out for you and get that water to your system in the media bed or biofilter ASAP.

If you can’t find a good bacteria source there are plenty of commercial products out there. These can be pricey especially in large quantities and not always reliable with live bacteria. Things like shipping in summer and winter could affect the bacteria in transit so if possible try and find an existing source of live bacteria in your area. If you can’t here’s one we’ve used in the past with good results.

Notes On Water Quality Needs For Cycling Aquaponics Systems

Bacteria are living things and they need their environment to be controlled within certain parameters in order to thrive, just like our fish and plants. Frist, we want to make sure our water is chlorine free. If you only have city water you are going to want to off-gas it or ideally use a filter like this to remove the chlorine, as it will kill your bacteria. This stands for all water additions to the system, not just on your initial fill up.

You will also need to monitor your water temperature. Nitrifying bacteria thrive between 25-30 degrees Celsius (77-86 Fahrenheit). At around 18 Celsius (65 Farenheight) your bacteria populations growth rate cuts in half and it stops altogether at 5 Celsius (40 Fahrenheit). They will also stop producing and die off at 50 Celsius (120 Fahrenheit). The good news is so will your fish and plants, you bacteria thrive in a temperature range that is suitable for most fish and plants you’d want to grow in an aquaponics system.

Cycling Aquaponics Systems Conclusion

Cycling an aquaponics system can be stressful for some because it’s not a process they are used to. There are pros and cons to each method but the big takeaway is just to have patience. This is a process that happens naturally every day in nature and if you let nature take its course your system will cycle. Don’t let your angst to get growing amazing fish and plants let you get off on the wrong foot. Taking the time to properly cycle and add those things at the right point will make the difference between an easy to maintain start to your system versus a hectic and stressful start where you are trying to accommodate for the poor conditions for the plant and fish. Be patient. Establishing an ecosystem takes time but the rewards will be a stable and productive system for as long as you are gardening.

Cycling Kits

If you want to take the guesswork out of sourcing your bacteria we do offer cycling kits in our shop. These kits include detailed instructions on how to cycle your system with the kit. They also include your ammonia to kick start the nitrogen cycle, beneficial bacteria to speed the cycle along and soluble seaweed extract to kick your system off with a nice nutrient profile so you get great growth right out the gate.

Our small cycling kit is perfect for those small DIY systems for those just starting out with a small system. For tank sizes of 100 gallons or less this is the kit for you.

Our medium cycling kit is geared towards medium sized systems likely those of you growing in a basement or backyard. For tank sizes of 100-300 gallons, this would be for you. A classic system here would be one that has an IBC tote for a fish tank that feeds a couple of media or raft beds.

Finally, our large cycling kit is for those with larger backyard systems and commercial growers. Depending on the size of your system you may need multiple kits. These are for systems 300-500 gallons. If you have a system larger than that it will either take a bit longer to cycle or you can buy multiple kits to match your tank(s) size and get a cycle in 7-10 days.

Happy Cycling!


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