The top 10 reasons why your aquaponics system isnt cycling

Establishing the nitrogen cycle, AKA ‘cycling’, is the hardest, most frustrating, part of aquaponics, in part because the activity is all invisible to the naked eye. Aquaponics cycling, however, is the most crucial and probably the most difficult part of aquaponics – but it really isn’t that hard if you can be patient! We hope that the nitrifying bacteria are finding our system, and then moving in and reproducing, but the only way that we know what is happening is through sometimes subtle changes of color in a test kit test tube. And when that test tube stays the same color day after day, sometimes week after week, it is very frustrating.

aquaponics cycling

Over the past few years of handling customer calls about aquaponics cycling we’ve developed a checklist of what to ask to help them identify the problem and cycle successfully. Hopefully you will see the solution to your own cycling mystery somewhere on this list.

  1. Temperature – During the colder months of the year, this is the number one issue we see, especially with people who are cycling without fish. The optimal temperature for bacteria reproduction is between 77-86 degrees F (25-30 degrees C). At 64 degF (18 degC) their growth rates is decreased by 50%. This means that the rate at which you cycle will be twice as long as it would be with warmer temperatures.
  2. pH Too Low – We had a call just yesterday from someone who has spent the past two months cycling with no trace of nitrites or nitrates. The average temperature of his system was between 65 and 70, so that could have had something to do with it, but when we asked him what his pH was he said 4.0! That is essentially an acid bath and there is no way that the nitrifying bacteria are going to colonize in that kind of environment. Bacteria actually prefer a pH closer to 8.0. While this is too high for your plants to be happy, during cycling the bacteria are the main focus so targeting a higher pH than you will want during the rest of your system’s life makes sense.As an aside, if you are using the API Freshwater Master Test Kit, and you see a reading of 6.0 that means that your water is at 6.0 or below. You might want to find another means to test to an even lower range to see what your actual, true pH reading is.
  3. Chlorine – This chemical is added to municipal water supplies for sterilization (i.e.,to kill the bacteria). It is easy to remove because it dissipates from the water as a gas. If you don’t already have a dechlorinating filter on your incoming water supply you can get rid of chlorine by simply holding the water in a separate tank for a day or two. Oxygenating the water using an aerator will speed up the process.
  4. Chloramine – While you can assume your city water supply has chlorine in it, chloramine is more rare. But it is also much more difficult to get rid of. There are two ways that I know of. The first is a double mechanical filtration method where you send the water through both a charcoal filter and a reverse osmosis filter. The second is to remove it chemically by adding a product such as ChlorAm-X. If you are using the chemical method you should do this in a separate holding tank before the water enters your aquaponics system.
  5. Stop Adding Ammonia – The next problem we see only occurs during fish-less cycling, and the scenario unfolds as follows. You add enough ammonia to reach 4.0 ppm then you start testing your system every day. After a while the ammonia disappears and nitrites show up. Good news! The problem starts, however, when you don’t replenish the ammonia. Think of the ammonia as food that you set out to attract the first set of nitrifying bacteria (nitrosomonas), and those bacteria come to the party bringing the food (nitrites) for the second set of bacteria (nitrospira). If the food runs out, the party is over and everyone goes home! You need to keep up a steady supply of ammonia in the front end of the process to keep everyone happily reproducing and colonizing your system. That steady supply can come either from an ammonia compound or from the addition of fish to your system.
  6. Too Much Ammonia – Some aquapons believe that ammonia levels higher than 6 ppm will actually retard the cycling process. Some don’t. I don’t know enough to form a strong opinion either way, but I thought I would add it to the list of possibilities.
  7. Sterile Environment – Occasionally we find a system that is being started in an indoor environment that is so shut off from outside air and a natural supply of nitrifying bacteria that it will never cycle on its own without the addition of purchased bacteria.
  8. Lack of Oxygen – Nitrifying bacteria are aerobic. The more oxygen you have flowing through your system the faster your system will cycle. Be aware that this is challenged by #1 above. Liquids at higher temperatures have a harder time holding gas, so if you are heating your water to encourage bacteria growth be sure to pump up the oxygen as well.
  9. Time – Cycling is a natural process that we can certainly encourage by establishing favorable conditions, but after that Mother Nature is on her own schedule. You might be doing everything right, and the bacteria just need a bit more time.
  10. You really are cycled; you just don’t know it – This is my favorite, because it is so easy to fix and the customer is usually delighted to discover that his problem was not really a problem at all! The instructions for your test kit need to be followed to the letter. If you don’t follow them, you won’t get accurate readings. The Nitrate test is by far the most complex, and therefore the most likely to tell you that you don’t have any nitrates when in fact you actually do. Do yourself a favor. Read and carefully follow the instructions!

Aquaponics cycling of a system can be a trying time, but the good news is that once you are fully cycled, you can safely add fish and plants and will never need to go through this again! Good luck.

17 thoughts on “The top 10 reasons why your aquaponics system isnt cycling

  1. One of my fish tanks is making foam on top of the water and I am seeing a lot of slime in the water. Any ideas what may be causing this? I have about 25 small gold fish in the tank. I recently added some white distilled vineger to bring the PH down but it is still high at about 8. My plants are doing well. Thanks for a reply.

  2. Hi Silvia

    I have set up two aquaponics tanks using IBCs. I am based in India and had to order the water testing and start up kits from the US and had a long delay in receiving them. I started cycling blind and just let the water cycling for 6 weeks blind, which was not ideal!

    I managed to get 10 fresh water shark that are apparently very hardy but the shop was shutting down so I had to take them and put them in the tanks at the same time as receiving the testing kits. They have been in the tanks for about 2 weeks now. 5 sharks are in each tank.

    One tank is looking good showing 0.25-0.5 ammonia level, 0 nitrites and 80 ppm nitrates. The water is clear and algae has formed in the tank. The other tank is not looking so good. Ammonia levels are 0, nitrites 0 and nitrates 0. The water is very dark green. The ph level also seems to shot up to 8.5-9.5 in a couple of days. I have been using ph down to bring it back down to about 7. Good job that sharks can live in any level ph water and I have not killed any yet!

    What course of action would you recommend to start developing the biological filter in the second tank?

    As I learn more I realise I have made a bit of a hash of the cycling process and now need to work out how I can save the situation!

  3. Pingback: Construction Update | DWC rafts and system is cycling | Our Farm This Week . com

  4. I started with fish instead of ammonia. Is it safe to add ammonia to my system in small amounts to speed up the process or will this likely kill my goldfish. I have 15 goldfish in about 13 gallons of water and aboout the same volume of river rocks above. I am keeping the temp at about 80 deg and have a bubbler with a large air stone in the fish tank.

    • Anthony, you only need to add more ammonia if your fish aren’t producing enough (about 2 – 4 ppm) and given the stocking density you have I can’t imagine that is the case! What would speed it up, however, would be to add nitrifying bacteria, such as what we have here.

  5. Hello, i have been cycling my system for about six weeks. i have a 200 gallon tank and a constant flow bed. i have no filter. its made of a 300 plus gallon ibc tote. i added water plants and fish guano all at a the same time and let it cycle…i figured if i was gone use fish poop later this would fish less cycle with the same product the fish would be producing in the future. the plants have grown a bit and look healthy but no as much growth as i would like. i have two airation tubes in the fish tank and a 325 gph pump.. after the fish guano stopped being cloudy in the water and it cleared about a week and a lot of smell later it seemed fine. i did not test ammonia or nitrite levels just ph. it was around 7. i said f*$# it and put in 100 med gold fish to see what would happen….they all died over night…so i got ammonia test kit. its thru the roof. over 8 ppm. i figured obviously its not cycled and i need bacteria to start eating the ammonia… i was gone build my own gravity fed bio filter to a sump tank and take the pump out of the fish tank. but I’m having plumbing issues. ibc totes have special threads on the lower out put nozzle and i need to wait for a delivery. so in the mean time i hung a bio filter media in bio filter bag and hung it in the fish tank at the top edge….. a week later and still my ammonia is high high. and my plants are staying small yet healthy. I’m worried about the constant flow bed but i read on this site that little difference can be seen between systems with bell syphons…although my strawberries did have root rot the rest do not. guide me….please

    • Hi Adam. There is a lot here to respond to, but I’ll try to hit some of the key items. First, I’m not a big fan of constant flow beds in a big system like yours. You must have read that on a different site – I’d rather see you flood and drain using a bell siphon. Those root rot issues will disappear. Second, you should dilute down the amount of ammonia in your system by doing a partial water change of at least 1/3 of your volume. Shoot for a level of about 4 ppm. Third, buy some bottled bacteria to get the process moving faster – – then keep an eye on ammonia, nitrite and nitrate. You will want to keep the ammonia at at the 4.0 level until you get fish (living) in there so you are constantly feeding the bacteria that is being established. Once both your ammonia and nitrites disappear, and you see nitrates start to rise it is safe for fish.

      I hope this helps.

  6. I recently bought a farm that has an aquaponic greenhouse. It was not being used and in need of repairs. There are about 20 bluegill in the 4000 gal tank. I rinsed themedia to remove excess gunk raised the beds and replumbed everything. Started cycling about 3 weeks ago and haveplanted the beds. Everything was progressing and nitrates were increasing. Thenfor no apparent reason the nitrates disappeared. They have beenaround 5 for the last few days. Any ideas? Usingyour cycling kits.

    • Hi Cindi. Generally the nitrates disappear because the plants are consuming them. Have you replanted the grow beds?

  7. Yes planted the beds over 2 weeks and finished them about a week ago. Should I remove some plants or will it catch up? I’m adding ammonia daily still and thenitrites are slowly dropping.

  8. Hi Silvia, I took a shade over 6 weeks on a fishless cycle I waited another week still checking water all test hit the marks where they need to turned temp down to 75 did a 20 % water change and bought fish . I bought 10 feeder gold fish for starts with in 5 days I have one left and it looks like it’s about to go. I payed .27 cent a piece for them seems cheap don’t it don’t know if I just bought sick fish or there is something else wrong with water that I can’t test . Any clues to what you might think it is ?

    • Hi Alan. Feeder goldfish are raised to be someone else’s dinner, so the standards for being healthy when you buy them are far less stringent. Most of them would probably have died no matter what your water chemistry.

  9. Hi Sylvia,
    My son has an aquaponics unit. On a recent visit he mentioned his plants are not thriving. They have a light yellowish green appearance and have stunted growth. His tank has a algae growth on the sides of the tank, fish look OK but there is some algae on the grow bed. Not having any aquaponics experience I didn’t have any advice to give except I felt the nutrient balance was out but at a loss to advise him on what to do to rectify this. Do you have any advise please?

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