Starting Up (Cycling) an Aquaponics System Using Fish

What follows is an article that was published at Growing last month as part of a series I’m writing on “Aquaponics How To”. I hope you find it useful!

If you have been following this series on how to build a media based aquaponics system, you now have your aquaponics fish tank and grow bed interconnected by flood and drain plumbing which is ready to be powered by a pump. Your grow bed is filled with the grow media and the fish tank is full of de-chlorinated water. Now it’s time to move into the living elements of your system, starting with establishing the nitrifying bacteria.

Bacteria are the magic that takes the unusable aquaponics fish waste and creates a near perfect plant fertilizer. In this article and the next, we will demystify the process of establishing a beneficial bacteria colony in your aquaponics system. This process is often called system “cycling”. Today I’ll talk about cycling using fish and next month I’ll go into how to cycle without fish. By the end of these two articles, you will fully understand what you MUST do to initiate cycling and to ensure its success. You will also understand what you CAN do to both make the process less stressful for your fish and your plants, and to speed up the process.

What is Cycling?

Cycling starts when you (or your fish) first add ammonia to your system. Ammonia (chemical formula NH3) is a compound made of nitrogen and hydrogen. It can come either from your fish or from other sources that we will discuss next month. Ammonia is toxic to fish (more on this later) and will soon kill them unless it is either diluted to a non-toxic level or converted into a less toxic form of nitrogen. Unfortunately, nitrogen as found in ammonia is not readily taken up by plants, so no matter how high the ammonia levels get in your fish tank, your plants will not be getting much nutrition from it.

Aquaponics CycingThe good news is that ammonia attracts nitrosomonas, the first of the two nitrifying bacteria that will populate your system. The nitrosomonas convert the ammonia into nitrites (NO2). This is a necessary step in the cycling process; however, nitrites are even more toxic than ammonia! But there is good news because the presence of nitrites attracts the bacteria we are truly after nitrospira. Nitrospira convert the nitrites into nitrates, which are generally harmless to the fish and excellent food for your plants.

Once you detect nitrates in your water and the ammonia and nitrite concentrations have both dropped to .5 or lower your system will be fully cycled and aquaponics will have officially begun!

The Importance Of Testing Tools

You must have some way of telling where you are in the cycling process, typically a four to six week endeavor. Specifically, you must monitor ammonia, nitrite, and nitrate levels as well as pH so that you know that all these elements are in range. If they are not, you may need to take corrective action. This is also the only way that you will know when you are fully cycled and ready to add more fish (or your first fish if you have been cycling with no fish at all). Plus, watching the daily progress of the cycling process is fascinating and something you can only see through the lens of a test kit. By the way, once you reach the point that your system is fully cycled, you will need to do much less monitoring than during the cycling process. So get through the cycling process and look forward to reaping the fruits (or should we say the fish) of your labor.

IMG_0388To do their testing, most aquaponic gardeners use a product by Aquarium Pharmaceuticals Inc. called the API Freshwater Master Test Kit. This kit is easy to use, is inexpensive, and is designed for monitoring the cycling process in fish systems.

You will also need a submersible thermometer to measure your water temperature. Temperature affects both the cycling rate and the health of your fish and plants once you are up and running. See more on this below.

Cycling with Fish

Ammonia (NH3) is the catalyst that starts the cycling process. You must have some means to feed ammonia into the system so that you attract the bacteria that are at the heart of aquaponics.

There are two ways to introduce ammonia into your system with fish and without (fishless). Today we will talk about cycling with fish, and tackle fish-less cycling in the next article.

The Ammonia (NH3)

I used fish to cycle my first aquaponics system and I suspect this is how most people approach cycling. In some ways it is the easier of the two methods because there are no extra inputs, but it is definitely the more stressful of the two options because live critters are involved.

The idea is to add fish on day one and hope that they live through the cycling process. The challenge is to get the system cycled fast enough that the ammonia concentration from the fish waste drops to a non-toxic level before the fish succumb to exposure to their own waste. I strongly recommend that you don’t stock to your tank’s mature capacity (1 lb of fish per 5 – 10 gallons of water) but to less than half that. You might also want to consider these fish as “sacrificial” and perhaps use goldfish from the pet store, which are fairly tolerant of ammonia, rather than the tilapia with which you may ultimately envision stocking your tank. Also, do not feed these fish more than once a day and only feed them a small amount even then.

Fish excrete ammonia through their gills as a bi-product of their respiratory process. Without dilution, removal or conversion to a less toxic form of nitrogen, the ammonia will build up in the fish tank and eventually kill the fish. In addition, ammonia (NH3) continually changes to ammonium (NH4+) and vice versa, with the relative concentrations of each depending on the water’s temperature and pH. Ammonia is extremely toxic to fish; ammonium is relatively harmless. At higher temperatures and pH, more of the nitrogen is in the toxic ammonia form than at lower pH.

Standard test kits measure total ammonia (ammonia plus ammonium) without distinguishing between the two forms. The following chart gives the maximum long-term level of ammonia in mg/L (ppm) that can be considered safe at a given temperature and pH.

Water Temperature

pH 20C (68F) 25C (77F)
6.5 15.4 ppm 11.1 ppm
7.0 5.0 3.6
7.5 1.6 1.2
8.0 0.5 0.4
8.5 0.2 0.1

You will need to monitor your tank water daily during cycling for elevated ammonia levels. If those levels exceed the levels on the chart above you should dilute through a water exchange by pumping out up to 1/3 of your tank’s water and replacing it with fresh, de-chlorinated water.

Adjusting pH

During cycling, especially with fish, you should try and keep your pH between 6.0 and 7.0. The range does not go below 6.0 because most fish prefer slightly alkaline water and few are happy below 6.0. The range does not go above 7.0 because of the ammonia toxicity issue described above (higher pH readings suggest higher ammonia concentrations). So how do you keep pH in such a tight range?

The first rule is: Whatever you do to adjust pH in aquaponics – Do it slowly! Fast, large pH swings are very stressful on fish and will be much more of a problem than having pH that is out of range. Target shifting your pH reading no more than .2 per day and you should be fine.

The safest way to do this is to use our AquaDown pH Lowering Solution. Raise pH either by using our AquaUp pH Raising Kit or by alternating alternatively use calcium hydroxide – also known as “hydrated lime” or “builder’s lime” with potassium carbonate (or bicarbonate) or potassium hydroxide (“pearlash” or “potash”). Don’t use citric acid as it is anti-bacterial!

Typically, you will be trying to keep pH down during cycling, and then once your system is cycled you will probably notice that the pH will fall and you will then need to switch to keeping it up. You will probably find that it is easier to increase pH than it is to decrease it. The ideal pH of a mature aquaponics system is 6.8 – 7.0. This is a compromise between what the plants prefer, i.e. a slightly acidic environment of 5.5 – 6.5, and what the fish prefer, i.e. a slightly alkaline environment as we discussed before.

The Nitrite (NO2)

Nitrite is to fish like carbon monoxide is to air breathers. The nitrite will bind with the blood in place of oxygen and keep the fish from getting the oxygen it needs. Fish poisoned with nitrites die of what is called “brown blood disease”. If the nitrite levels in your tank rise above 10 ppm while you are cycling your system with fish, you should do a water exchange as discussed above, but you may also want to add salt to the system in order to further protect the health of the fish.

Do this by adding salt to the system to at least 1 part per thousand (1 kg of salt per 1000 liters of water) using non-Iodized salt. Avoid table salt since it contains potentially harmful anti-caking agents. You can use cheap pool salt or water softener salt available at the grocery or hardware store, but the best product is salt specifically formulated for fish. Make sure to dissolve it completely in a bucket of water before adding it to the fish tank since un-dissolved salt crystals on the bottom of a fish tank can burn a fish that rests against them. Stop feeding your fish until the nitrite levels decline below 1.0 and aerate as much as possible.

How might salt (sodium chloride) help? Sodium Chloride helps mitigate nitrites because the chloride ions bind with the nitrites and thereby help keep some of the nitrite out of your fish.

Adding Plants

seed starting plugI recommend adding plants to your new aquaponic system as soon as you start cycling. Plants can take up nitrogen in all stages of the cycling process to varying degrees; from ammonia, nitrites and nitrates, but they will be happiest when cycling is complete and the bacteria are fully established because so many more nutrients become available at this stage.

When plants are first transplanted, they focus on establishing their root system in their new environment. You may initially see some signs of stress – yellowing and/or dropped leaves – and you will probably not see any new growth for a few weeks. This is fine. Adding plants to your system right away lets them go through the rooting process early on and readies them to start removing the nitrogen-based fish waste from your aquaponics system as soon as possible.

I recommend you use some Maxicrop to get your plants off to a good start during cycling. Maxicrop is derived from Norwegian seaweed, is organic and is used primarily as a growth stimulant, especially to enhance plant root development. It is extremely effective at giving plants a “leg up” after being transplanted into your new aquaponics system, is absolutely harmless to the fish, and probably beneficial for the bacteria. You can find Maxicrop in garden centers, hydroponic stores, and online in both liquid and dry form.

While there are no hard and fast rules about how much Maxicrop to add during cycling, I recommend about a quart of the liquid product for every 250 gallons of water. It will turn your water almost black but don’t worry; this will clear up after a week or so.

Speeding Up the Process

Cycling is in some sense akin to any hunting activity that uses a lure. We start by putting out the ammonia. This attracts the nitrosomonas bacteria which in-turn produces nitrites. The nitrites attract the nitrosprira bacteria which produce the nitrates that are harmless to the fish and delicious to the plants. These two beneficial nitrifying bacteria are naturally present in the environment.

As I stated earlier, this process will take four to six weeks if done with fish, or as little as ten days to three weeks if done fishless. But what if you could speed that up significantly? What if instead of waiting for the bacteria to show up to the party, they actually are part of the party to begin with? You can do this by introducing nitrifying bacteria into your aquaponics system.

Adding Bacteria

While there are many ways to do this, they all boil down to two basic strategies: use bacteria from an existing aquaculture or aquaponics operation or from a near-by pond or instead, purchase bacteria from a commercial source.

Good sources of beneficial bacteria from existing systems are ranked here, leading with the best:

  • Media from an existing aquaponics system
  • Our Microbe-Lift Nitrifying Bacteria product
  • Filter material (floss, sponge, biowheel, etc.) from an established, disease-free aquarium.
  • Gravel from an established, disease-free tank. (Many local pet and aquarium stores will give this away if asked.)
  • Other ornaments (driftwood, rocks, etc.) from an established aquarium.
  • Squeezings from a filter sponge (any pet and aquarium store might be willing to do this…)
  • Rocks from a backyard pond with fish in it

Managing Water Temperature

Water temperature also has a dramatic effect on the speed of cycling. Their optimal temperature is between 77-86° F (25-30°C). At 64°F (18°C) their growth rates is decreased by 50%. At 46-50ºF (8-10°C) it decreases by 75%, and stops all together at 39°F (4°C). It will die off at or below 32ºF (0°C) and at or above 120°F (49°C).

Cycling with Fish – Conclusion

While cycling with fish is the most widespread and straightforward of the cycling techniques, it is stressful on your fish and therefore somewhat stressful for you. But it certainly works. Next month we’ll go over another technique called Fishless cycling that uses pure ammonia to cycle your system.

Either way, it’s time go get up and grow!

42 thoughts on “Starting Up (Cycling) an Aquaponics System Using Fish

  1. Sylvia,

    I have loved reading all of your articles and have found them to be extremely helpful. I am almost finished setting up my first Aquaponics system. Currently the system is 100% cycled and is home to 8 blue tilapia and an plant-less, gravel filled, 10′ x 3′ grow bed. I planted my starters a little late because I was waiting for the seeds to arrive but now my burning question is how big should my plants be before I add them to the system? I plan to grow leaf lettuce, spring mix, kale, and basil for starters. Many of my plants are about 2 inches tall currently and seem quite healthy. Are they ready to be put into the gravel in my grow bed or do I need to wait until the roots are more developed?

  2. Pingback: Cycling in Aquaponics | Team One

  3. Sylvia,

    I just setup my system on the 17th and started the cycling process on the 21st. My pH is 8.0 as I live in Phoenix AZ. I haven’t added any plants yet but I do have four 8-10 inch goldfish. I have about a 700 gallon system and wanted to know approximately how often will I need to add maxicrop?

    Thanks in advance,


    • Hi Samson. You should just need to add Maxicrop once or twice as a nutrient booster until your fish take over feeding the plants. Right now you don’t have enough fish for a 700 gallon system. Were you planning on adding more? You could use between 70 – 100 lbs of fish in there.

  4. Sylvia,

    Wow you responded very quickly. I didn’t expect a response so soon given the holidays but I sincerely appreciate it greatly. I didn’t know how many fish I should start with. It appears that need a bit more to really get the ammonia rocking. I am using a 275 gallon IBC tote as the fish tank so what would your recommendation for fish stocking density to really kick off the cycling process?

  5. I’m looking for the right medium to start seed, how to you transition to water and not get starting medium in your water, coir?
    Also to Loo what is an IBC tote and where do I find one?

    • KLEE,

      I have some hydroton which I put in 2-in net pots. I simply added the seeds towards the middle of the hydroton and had no issues with the seeds sprouting. IBC is intermediate bulk container.

      • To clarify, the net pots are in my raft bed and the seeds started germinating a week or so later. Now pretty much all of the 42 seeds I potted have sprouted and I am extremely excited.

  6. Sylvia,
    I’m starting my first indoor aquaponic system. I was confused about adding the plants. Should I put my plants at the same time I start cycling ? Is the seaweed technique the easiest to start cycling (instead of adding ammonia) ?

    Also, my system is very small (45-50 gallons). How many goldfish do you recommend to put in there?

    Thank you very much !

    • You can put them in at the beginning with the seaweed, or wait until cycling is complete. The choice is really up to you.
      Seaweed only has a small amount of ammonia in it…it is mainly there to get the plants off to a good start.
      If you are primarily growing herbs and flowering plants, we recommend stocking your fish tank with 24”‐36” of fish. If you are growing a mix of house, shade and flowering plants, we recommend stocking with 16”‐24” of fish. These measurements are for the total number of inches all fish. Fish
      are measured from their nose to the base of their tail.

  7. Hello Sylvia,

    I started my aps slightly over a month ago. I have a 80 gallon tank with a 2ft by 8ft grow bed, there is roughly 20 2-3inch goldfish. My goldfish keep dying from Ich and my leaves on my plants are turning yellow and haven’t really grown much. I tested my water earlier… ammonia- .25ppm, nitrate-5.0 ppm, nitrite-0 ppm, and pH-7.6ppm. Do you have any recommendations, thank you in advance.

    • Cassidy, you are still cycling, so your plants aren’t getting much food. You should add some Maxicrop to keep them alive and fed until your nitrates show up. Once they do, and the nitrites are zero, you will be fully cycled.

  8. Hi, I have a 500 gallon system with 4 4.5′ round growbeds. I just got it up and running with new water and granite media. I am fishless cycling. I’ve jumpstarted the system by adding bacteria from a friend’s established system. My initial ph was 8.0 with the tap water. I attempted to lower it and it got down to 7.8. After running overnight, it is now up to 8.2. Do I need to do anything or will it fall naturally as the cycle continues and I add the plants? Thanks!

    • Hi David. The pH will go down naturally, and honestly the bacteria, which is the main focus of the cycling stage, likes a higher pH anyway. My suggestion is to just leave your pH alone for now.

  9. Our system has been running now for 2 months. We have tomato plants that are growing but are yellowing.?? and they are getting little black spots on the leaves. Radishes are growing nicely. Lettuce is coming up from seeds and big established lettuce plants are thriving. Basil is growing and happy. parsley and italian plant just like it are happy and growing. Just yellow tomato plants. We have high intensity lights(4 bulbs). temp in the room is 70 and water temp is 70. Gold fish(40) are doing great.16 hours of light and the light is set at about 12 inches off the bed. Tomatos are about 10 inches high and quickly growing and blooming.The siphon is working great. The goldfish are about 3 inches long. Do I need more fish? I think so. I feed them twice a day. We have a rubber maid 50 gallon grow bed and a 150 gallon rubber maid fish tank.We have 200 red wigglers in the grow bed.Ammonia is close to 0. Tomato plants not happy.?

    • what are red wigglers, and how do you get them into the media bed? Are these just the worms that I can get out in my yard or garden?

      • Red wrigglers are the kind of worms you can get at bait shops, or you can find them by clicking here. They are different from the worms you find in your garden because they can handle substantially more moisture, so are much more appropriate for an AP garden.

  10. Can’t find Maxicrop locally. However, I can find a product called “Greenbelt Organics Seaweed 1 lb. Organic Powder Fertilizer Bag”, but of course this is powder, not liquid. Can this be used with my aquaponics system just like Maxicrop?

  11. I am setting up a aquaponics tank for the first time and can I use a sponge filter from another tank will that work ?

  12. We started an AP system about 10 days ago. The pH is stable at about 7.6, water temp. in 70’s, nitrites and nitrates are present, the nitrates are slowly rising BUT the problem is the ammonia. The ammonia level has not dropped: still sitting at 8ppm. Question is: is there any other way for getting the ammonia level to drop besides waiting for the bacteria to do its job or changing the water?

    • HI Wendy. Not really, unless you want to add a filtration system. Your ammonia is very high for cycling. I’d recommend a water change to get it down to the 2 – 4 ppm level, then either add external bacteria, or just wait for your system to cycle naturally.

  13. Cycling my aquaponics system with 5 goldfish 4-7” long indoors in a 110 gal stock tank, 45 gal growbed and an 18 gal filter. It’s been 3 wks and my ph is consistently 6.4 to 6.6 after three 30% water changes tho the ammonia remains at 4.0. I have two air stones in with fish and one in filter. Water is de-clorniated for water changes. Temps are around 74 degrees. Nervous about the high ammonia and low ph but not sure if I should bump up the water changes to every other day (now its about every 4-7 days), add ammo lock, turn off the air stone to filter, or add builders lime or baking soda to lower ph and at what amounts for this size? Fish are happy and I’m feeding only every other day tho not much.

    • Hi Carol. The best thing you can do is get your pH up. The bacteria like it close to 8.0, and will develop faster at that level. Avoid baking soda! It has sodium in it, which is bad for your plants. Best to use our AquaUp product.

  14. I will thank you! I will bump up the water changes and I added rocks and water from an existing cycled system. I also did ammo lock as the ammonia had climbed to 8 before the water change this am. Will test later in the day again. Water is nice tea color which is what it should be I’ve read. Fish seem happy and swimming around, I don’t get how they are alive.

  15. My ammonia is VERY high and I am concerned about my fish. I added a new grow bed to my system that is 12′ x 3′ It then dumps via siphon into a new float bed that is 10′ x 3′. That drains back into my sump tank which is a 55 gal barrel and a 44 Gal. barrel with a bridge siphon. Form there the water is pumped back into the fish tank. I also have a 4’x4′ original grow bed that i was originally using. However, I had to take that bed out of service to move it and then had to start it over. My fish tank is 250 gal. IBC and I have about 100 tilapia . My PH took a dive so it is down at 6 or below. My ammonia is at 8 (ouch) and has been there for about 2 weeks now. I have not lost any fish (yet). My nitrites are 0 and my nitrates are between 40 and 80. My plants are doing OK but have not really taken off. I am concerned that if I try to raise the PH the ammonia will become toixc. The temp in the tank is about 72 F. I replaced replaced about 100 gallons in the system today but it didn’t seem to change the levels. I am hardly feeding the fish at all. Should I add nitritefying bacteria? Should i attempt to change the PH? The water is clear and the fish are not acting stressed so i am kind of confused.

    • Hi Dennis. I have a few thoughts based on what you’ve said here. First, you need to bring your pH up because the nitrifying bacteria actually prefer a pH that is above 7. Just do it slowly, over a day or so, otherwise this will just add to the stress your fish are experiencing. And YES, add beneficial bacteria! It will jumpstart the process, which you could use right now! Also make sure the water temp stays between about 75 and 82 during cycling as that will also encourage bacteria growth. Good Luck!

      • Thanks so much! I have started raising the PH by adding egg shells to the grow bed. Would you suggest I do something more or faster? Will it hurt to also add MaxiCrop to help the plants? What brand or kind of Bacteria would you suggest I add?

  16. Thanks so much for your comments Sylvia! I added egg shells to the grow bed and my PH is now starting to move up although very slowly. Should I add anything else to increase the PH? Also, should what product should i use for the beneficial bacteria? Would this be the correct Microbe Lift Nite Out II – Nitrifying Bacteria ? Would it hurt to add Maxicrop to help the plants or should i wait on that? Thanks for your help!

  17. I’m planning on starting a very small aquaponics system using five 4′ goldfish that are normally kept in a small pond, but need to spend the winter in a tank. They have been there for about 1.5 months. The plants won’t be coming into play for at least a week, likely closer to two weeks. I don’t have any Ph or nitrogen levels for you to look at. Somehow the lady who was taking care of them before managed it without water testing supplies. The fish are currently living in a barebones tank with only a thermometer and filter. They seem to be doing just fine. Would that mean that the cycling process is already done, and I don’t need to go through this treacherous time? Should I be adding gravel to make more surface area for the bacteria?
    P.S. The fish aren’t mine, just mine to take care of. So I prefer an assurance of live fish as compared to a quick start up.

    • Hi Tyler. Unfortunately unless you do regular and frequent water changes the only way that I know of to achieve “an assurance of live fish” is to test pH and nitrogen levels. Get yourself a good aquarium test kit, like the API Freshwater Master Test Kit. Once you have done that you should aim to maintain your pH at around 6.8 – 7.0, your ammonia and nitrate at, or close to, zero, and a nitrate level of 40 – 100 ppm.

  18. Hello .. Sylvia aquatic plants are not available in the aquatic stores in my … Is it necessary? ..and Is there anything else I can put it in your aquarium me as plants tropical wilderness ^^ ..

  19. Several of us are trying to start a non-profit aquaponics business but we need to learn more about it than we can find in books or on the internet.Do you offer classes or can a person take a tour?

  20. Hi, I just started my aquaponics system a few weeks ago and have placed about 9 goldfish in the tank already. The fish have been in there about a week, but I just got the API Freshwater Master test kit today. My pH was 7.4, Ammonia about .25 ppm, nitrites 0 ppm, and nitrates 0- 5 ppm according to the color chart. How do I know when it is done cycling? or if it has really even started? Do I need to add more fish to help add more ammonia? If it helps my system is a blue, food grade, 55 gallon barrel, cut into two parts with the grow bed from the top part sitting directly on top of the tank and it is kept in my garage.

    • Hi Cait. The big question this time of year is how cold is it in your garage? Systems won’t really cycle when the water temp gets much below 60 degrees.

  21. Hello Sylvia. I am a STEM Elementary Teacher. I am currently planning a project based lesson on growing plants without soil. I am starting with a simple hydroponic lesson. I then want to expand it into aquaponics. I plan to have students research various designs and the methods used to running a successful system. I would love the students to build one though using goldfish, since they are cheap. Is there a website or design you recomment on an extremely small scale, thinking one plant, one or two goldfish, soda bottles or some other type of reusable materials (due to budget). Any ideas or can you steer me to other sites that might be better on a small scale. Also, would you be willing to have my students video skype or email you as a professional or expert in this field to answer questions or give them feedback on their ideas? I appreciate any help you can give me.



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