Cycling a New Aquaponics System. Quick Guide.

How to Cycle a new Aquaponics System.
Have your system built and the water circulating, the auto siphons are functioning and adjusted well. If you have decided to use a timer system for flood and drain, then your timed cycles should be functioning well. You have run the system long enough for the water to be clearing.  The water can be a bit dirty from loose dust on the clay pebbles or gravel, but it should start to clear after a few days.

Barra in a basket

Small Barramundi contained in a plastic laundry basket within the fish tank. This makes it easy to take the fish out and treat them in a salt bath if necessary.

Small Barramundi contained in a plastic laundry basket within the fish tank.  This makes it easy to take the fish out and treat them in a salt bath if necessary.

Adjust the pH to just below pH 7. Adjust using pool acid to bring pH down or hydrated lime to adjust pH up. Get some plants in there right away.  The plants will soon tell you if there is not enough nutrients.  Use some Maxicrop or Seasol seaweed extract to provide some nutrient for the plants.  It will not harm the fish once you have them in the system.
There are very small amounts of ammonia in these products, so the process of building a suitable colony of beneficial bacteria will be slow, but it is a very safe and gentle way of cycling your system. Be patient.  These are natural processes and they take time. If you feel you must  speed the process, then, in addition to the seaweed extract, add a VERY SMALL amount of Urea.  No more than 1 teaspoon per 1000 litres of water.
If you can obtain some pure ammonia then use that in preference to Urea.  Once again, very a small amount like 1 tablespoon per 1000 litres (250 gallons). I stress that my preference is not to use Urea.  It can be vicious and cause lots of problems if overused.

The beneficial bacteria are naturally occurring, and they will begin to multiply once there is ammonia present. One option t ensure you have a good number of the beneficial bacteria present is to add some water , 3 or 4 liters (1 gallon) from a disease free freshwater aquarium, or a friends Aquaponics system.  The beneficial bacteria will be in this water and will take up residence in your new system and begin to multiply and use/process the ammonia. After your system has been running for about two weeks and everything is going nicely…..add the fish of your choice.

Stock lightly for your first batch of fish. Don’t be tempted to have a lot of fish in the beginning. Remember , loads of aeration and a backup system. Conduct your usual tests for Ammonia, Nitrites,  Nitrates at the following frequency. Daily for pH and Ammonia. Every second day for Nitrites. When the Nitrites appear you will know that the beneficial bacteria are on the increase. A short period of time after that Nitrates should start to appear. Test for Nitrates every second day until you see them appearing.  Once you see Nitrates you know that your system has cycled. All the while test for Ammonia.  If it goes beyond 1.0 mg/L then carry out a one-third water change.
The good thing about having the plants in is they are capable of taking up some of the ammonia.  Once the system has completed the "cycling" process tests for ammonia should reveal very small amounts or even none at all on occasion. All the while test pH.  Try to keep it just below pH 7.   It is not uncommon to observe swings in pH during this early period.   Don’t panic and start chasing the pH.   Only adjust when you see a firm pattern developing, for example, if it stays at say, 8.0 for 3 days, adjust gradually down using pool acid or similar…….be gentle, adjust in small increments, until you get it steady just below pH 7.

Once your system is up and running and everything is just fine, if you want to introduce more new fish always quarantine them in a salt bath for a week before putting them into your main system.  Don’t risk bringing sick or infected fish into your working Aquaponics system.
Happy Aquaponics Murray.

Please note: I reserve the right to delete comments that are offensive or off-topic.

Leave a Reply, I love to hear from you.

19 thoughts on “Cycling a New Aquaponics System. Quick Guide.

  1. Hello Murray, I was wondering if the Seasol or Maxicrop for here in the states are harmful to fish. I have some starter goldfish and wanted to add Maxicrop this weekend. I am using a 330g Fish tank with a max capacity 175G sump tank (I keep the sump at 125G). The goldfish are kept in the sump tank since I am using your CHOP 2 configuration and don’t wish to actually raise Goldfish. Thank you and I love your videos.

  2. Hello Mr. Hallam, I have had standard gardens forever but wanted to start an aquaponics system. I have been doing research and gathering information for over a month. Got onto this blog about an hour, maybe hour and a half and learned more practical info than I did the whole previous month. I want to thank you for this. Hope to have an operational, (small scale) system up and running by early May. I’ll be back…

  3. I am starting my aquaponic first the growbed i am fitting the drainpipe just one inch below from the gravels immers in water all time. so please tell me how i can fix the drainpipe.

  4. Hi Murray,
    I am just filling my system, 4500 lts, and would like to know your views on using a Koi Carp instant bacteria, it seems get get good reviews from the fishy people but nothing on the aquaponics front.
    Thanks for all your help so far, Cheers, Simon, London

    • Hi Simon, Ok if you want to but really unnecessary. The beneficial bacteria are naturally occurring and will come if the right conditions are there.

  5. Hi Murray,
    I have learned so much from this website, especially about the 3 nutrients missing that need to be added. Iron, potassium and calcium. Your videos show how to add the first 2, but what type of calcium do we need to use and how much?

    • Hi Johan,
      Calcium is added when there is a need to buffer the pH. By using hydrated lime to buffer the pH upwards calcium is also taken care of. Hydrated lime is very high in Calcium. I hope this helps. Regards Murray

  6. Hi Murray – Still following your exploits. Pls clarify the “salt bath for a week”. Won’t that kill the fish? Cheers, Guy

    • Hi Guy,
      No it will not. All freshwater species I have worked with are very salt tolerant and do well with salt treatments. I am quick to caution that may not be the case with every single freshwater species out there in the world. For example, I would be cautious in using salt with Trout. I have not kept Trout but hope I am fortunate enough to get some one of these days.

  7. Murray, your the reason I got into aquaponics. Thank you. Joe in central Fl. If your ever back in the area email me and come by . I’m very close to green acres and Morningstar fisheries.

    • Thanks Joe,
      I will be over that way in March 2016. So, love to meet then.
      Hope all is well with you.


    • It works best at around 23c but can work down as low as 12c. It is difficult to get a system to completely cycle at low temps.