Aquaponics 101 Part Four: System Start Up

This is the fourth in a series of posts that are going to teach you most of what you need to know about Aquaponics. These posts are part of a book we are writing and will be selling on our website. So, if you’re curious about the most amazing food growing technology on the planet today, watch for this series of educational posts on Aquaponics and please, become interactive by making comments or asking questions. Given the state of our Union, the motto on our website is becoming more important than ever–“Time To Grow Food”.

In Part One, “The Process”, I wrote about what Aquaponics is and why it is important to Preppers (those preparing for what is about to come down the pike), the fact that you can grow food for you and your family year round as long as your Aquaponics system is in the proper environment. I also gave a description of the biological processes involved that make Aquaponics work.

In Parts Two and Three, “The System”, I wrote about the components of a basic system. To quickly review, I wrote about the need for a bio-filter and that it is usually combined with the grow bed to form a single Aquaponics component called the grow bed, which is the most important part of an Aquaponics system. I told you about the grow bed media, the grow bed shape, and that you need about one gallon of grow bed/bio filter volume for every gallon of fish tank volume and the reason for this ratio. I discussed the need to flood and drain your grow beds four times an hour and how to properly size your water and air pumps.

I’m now going to focus on how to get your system up and running, but first we need to talk about water. To your Aquaponics system, water is life. The water in your system contains elements that provide life to the various organisms living in your system. These organisms include the fish, bacteria and the plants. The one element in your water that is essential to all of these organisms is oxygen in the form of dissolved oxygen, or “DO”. As mentioned earlier, an Aquaponics system with ample DO (dissolved oxygen) will perform much better than one that is lacking in this life giving element.

At all times, you should strive to keep your DO levels above 6 ppm (parts per million). The only way to know the value of DO in your system is to measure it, and the only way to do that is to have a rather expensive DO meter. The design guidelines I have given you in the previous posts will assure that you achieve this goal so the actual purchase of a DO meter is not crucial. Most backyard Aquaponics hobbyists don’t pay much attention to DO levels because of this DO meter price. They are investing minimal money into their systems, and the price of a DO meter is not in their Aquaponics budget. I understand this; but for me, as a researcher, I felt that I needed to swallow hard and pony up the cost once I was convinced of the importance of DO levels in the system. Not knowing what my DO levels were and what I could do to affect the DO levels was more than I could stand. As I wrote in Part One, fish need oxygen to live. The bacteria also need oxygen to live and to convert the fish wastes into usable nitrates. The plants need oxygen to grow. Some of the plant oxygen comes from the DO in the water, which brings us back to the water.

The water also has a pH, which stands for the Power of Hydrogen. The word, “Power” here is a mathematical function where each level is ten times the previous. So, pH is a logarithmic scale, base 10, or power of ten. The lower on the pH scale, the more acidic the water and the higher on the pH scale the more basic. Bases can be thought of as the chemical opposite of acids. A strong base will raise the pH of water toward 14. Seven on the pH scale is neutral. Notice I said basic (base), not alkaline. Some would argue that they are the same; but in dealing with pH and water quality, there is a difference. Alkalinity is a measure of the alkaline buffers found in the water. These alkaline buffers are dissolved minerals, like calcium, that keep the water’s pH at a higher than neutral seven pH. Any attempt to lower the pH of water by adding in an acid (pH down) will be countered by these alkaline buffers and not allow the water’s pH to change and go to a lower number. You might see a sudden change after adding in an acid, but it won’t last and will soon rebound back to its higher pH value.

When the fish add their waste to the water, the bacteria release hydrogen from the ammonia in the waste. This hydrogen is one of the building blocks for acid, and you will see a decrease in pH. The alkaline buffers will attempt to raise the pH; but with the continued release of hydrogen, the water’s pH will achieve a tug-of-war balance that is lower than the pH of the water before the bacteria started doing their job. As the fish grow out, and you feed them more food, they will produce more waste, and the bacteria will grow thereby producing more nitrites and nitrates. In the process, more hydrogen is released from the fish waste ammonia. This will continue to pull the pH to a lower, more acidic number. Where your pH level starts partly determines where it ends up. You will be continually adding water to the system to replace evaporation and plant uptake. This will slowly increase your dissolved solids, including alkaline buffers, because they do not evaporate with the water.

In our system, we started with a water pH of 7.6; and as the fish grew out, it went to 6.8 and stayed there until this winter when another pH influence made it go much lower. The previous winter we added a natural gas blue flame heater to heat our greenhouse and add some CO2 to the air to help the plants grow. This winter, the second one in this greenhouse, we experienced some very cold nights for our location and the heater was on a great deal of the time. It kept the temperature at a safe level but added an extra amount of CO2 into the greenhouse. The aeration pumps we use draw from the ambient greenhouse air, including the added CO2, and feed it into the fish tank water. This extra CO2 mixed with the water creating carbonic acid, and the pH plummeted all the way down to 5.8.

Once we realized what the source of our low pH was, we ran a tube outside the greenhouse and fed the aeration pumps from the outside air. Now the pH is back to a nominal level. Before we discovered this “fix”, the emergency action was to do a partial water exchange to bring the pH back up to higher levels and reduce the feeding level until we figured out the problem and implemented the solution. Lesson learned.

This little story is to give you an example of what it is like to be an Aquaponics farmer. Just when you think you have it all figured out, it will throw you a curve, much like life.

Because the water continuously evaporates, it leaves behind minerals. The solid fish waste is also mineralized so the mineral content of the water continues to increase over time as measured by a Total Dissolved Solids (TDS) meter. A high level of dissolved solids is generally not a problem, but this depends on the species of fish you raise. I am not going into this further here because there are just too many fish species to talk about them all. I don’t want to pretend to be a fish expert, nor do you have to be one. But, you do need to learn as much as you can about raising the species of fish you choose to populate your Aquaponics system.

We have found that a pH of 7.6 from the tap water is an acceptable number. It is very important that the water you use in your fish tank be free of chlorine and chloramines. Municipal water will always contain one or both of these. The best way to remove chlorine is to use a carbon filter designed to do just that. You can also just put the water in a separate bucket or open tank for a day or so, thereby allowing the chlorine gas to evaporate out of the water before transferring it to the fish tank. Because adding water is a repetitive chore for an Aquaponics farmer, this separate tank method becomes a hassle after a while. Adding a carbon filter and a float valve in your fish tank, connected to your tap water, is a way to reduce your work load and not chance letting your fish tank water get low.

If you have incoming water pH numbers in the eight plus range, then the best way to lower the pH is to use a reverse osmosis water filter. Reverse Osmosis is a process that uses a membrane with very tiny holes in it that allows water molecules under pressure to pass through it but not much else. Any molecule larger than the size of the hole won’t be allowed to pass through, but it will plug up the hole. After some use, the membrane will cease to pass much water through it as most of the holes become plugged.

There are two methods to remove the particles from the plugged holes. One is to flow water backwards through the membrane, thereby flushing out the problem particles. This is called a back-wash or back-flush, much like is done in a pool filter. The other way to keep the membrane clean is to use a tubular membrane where water is flowing through the tube under pressure from one end to the other. The pure water will pass through the membrane while the contaminants in the water are continuously flushed down and out of the tube through a pressure release. All RO water filters waste water; and in some municipalities, RO water filters may be regulated.

You take the RO filtered water, mix it with some carbon filtered water from the tap and use the mix to regulate the pH in your fish tank. This mix ratio requirement will change as the fish grow out. The ideal pH is about 6.8, plus or minus 0.3. So, a pH between 6.5 and 7.1 is acceptable for water in an Aquaponics system. Remember, the fish like their water pH high and the plants like it low.

You will need a water testing kit, and I recommend the API Freshwater Master test Kit. This is the number one preferred test kit by Aquaponics farmers. It will measure pH high and low, Ammonia, Nitrites and Nitrates. You can use the testing kit to make pH measurements, which will give you a ballpark range that is adequate. But the best way to measure your pH is with a reliable pH meter, one that is easy to calibrate and use. I know, I’m always finding ways for you to spend money on your system. So, tell me about a hobby where this is not the case. However, Aquaponics is more than a hobby. It is about growing your own food for you and your family, and you want to get it right because your life and the lives of your loved ones may depend on it.

Monitoring your pH with a pH meter is very simple and requires less than a few minutes to make an accurate pH measurement. I leave the pH meter probe in clean water, place it in the fish tank water and switch on the meter to tell me the pH to the nearest tenth when I wish to make a measurement. The meter probe only takes a minute or two to adjust to the fish tank temperature and give me an accurate reading. This allows me to see the slightest change and gives me a warning if something is out of the ordinary. Letting a pH meter probe dry out will cost you another probe, for they cease to function once they have become dry. I calibrate the probe using filtered tap water and adjust it to my known pH of 7.6 on a weekly basis.

I do not recommend adding pH up or pH down chemicals to your fish tank water, even if you get them from a fish store. They may contain elements that either are not friendly to plants or humans. Remember, this is an Aquaponics system, not an aquarium. I don’t care how much fish raising experience you have. What I have seen is that those coming from an aquarium background bring with them knowledge that they believe is beneficial, but it is often detrimental to their Aquaponics systems. The same is true for those coming from a hydroponics background. This is not aquaculture, or hydroponics, it is Aquaponics; and it has its own set of rules and requirements which are all about balance between fish and plants.

Another source of pH problems is gravel grow beds. You need to make sure that the gravel you place in your grow beds is both sterile and pH neutral. This is just another reason to use Hydroton. Hydroton is expanded clay balls that have been popped in an oven, much like popcorn. It is pH neutral, sterile and very easy to work with. I recommend the 8-16 mm mix size. It is sold in 50 liter and smaller bags. You can find it at any hydroponics store or on line for a better price, but ordering it on-line will add shipping and may prove to be more expensive. Some Aquaponics do-it-yourselfers go down to the local river or gravel pit and get gravel, put it in their grow beds; and they don’t have a problem. But from reading the fora, many end up with a serious pH problem from doing this. Some folks don’t backup their hard drive and have never had a hard drive failure either, until they do.

It will be necessary to keep your water temperature in a range that is healthy for your fish as well as your plants. For example, some species of Tilapia require the water to be around eighty degrees F. While other species of Tilapia can live in much colder water. Vegetable roots generally like the water to be in the sixty degree F range. You can see the water temperature conflict. Trout may seem like a good fish to raise because they do well in colder water; but they tend to take a long time to grow out and are sensitive to poor water quality. For a first time Aquaponics farmer, I would not recommend Trout. You might want to consider Carp if you don’t plan on eating your fish. Look into the fish species that is best for your climate and legal for your area. I’ll be sharing a lot more about the easiest fish for an Aquaponics farmer to raise, Tilapia, in a later post.

Once your system is assembled, the grow beds filled with media, the water is in place, the pH is balanced, the pumps are tested and the grow bed flood and drain timing is adjusted; you can now cycle your system. Cycling your system simply means that you want to turn on the water and air pumps and leave them on so you can grow some bacteria. By the way, once you have your system up and running, you never, ever, want to turn it off; not even for the night. First, you must get bacteria into your water; and here is where we get into an area of debate amongst those who have been into Aquaponics for some time. We all have differing opinions as to how to accomplish this task.

There are commercial products that claim to contain bacteria; and we supply (but do not sell) a bottle of this with our systems. However, we also state, right in the system manual that we make no claim of its viability. The logic is that bacteria cannot live in a bottle for any extended period without oxygen and ammonia constantly being fed to it. One source of this starter bacteria is your (or a friend’s) aquarium water. Take some of it and place it in your Aquaponics tank along with your water. However, in doing this, you will run the risk of bringing with it pathogens, which is not a good thing to do. The same is true for pond water.

Bacteria multiply once they are fed. Here again, we get into some tall grass of opinion. You must supply the bacteria with ammonia in order for them to multiply. This process will take at least two weeks before the system is considered “cycled” and ready for fish and veggies. One way to do this is to purchase chemically pure ammonia (keep it refrigerated) and very slowly (and carefully) add a diluted amount each day while measuring your system water chemistry. Do NOT use any animal urine, and especially not human urine, for these prolific sources of ammonia contain toxins, including prescription drugs (and perhaps nonprescription drugs) that you do not want in your Aquaponics system. Remember, we hope you are planning on growing organic fish and veggies in your system, so keep it pure and your fish alive.

In starting our first system, we added some of the bottled bacteria I discussed above. We then added some diluted pure ammonia. Later we added too much ammonia and killed off the bacteria that convert nitrites into nitrates (nitrosomonas). We knew this because we had very high levels of nitrites and zero nitrates. So, we exchanged some water an added more bottled bacteria and everything started to work. It would appear that the bottled bacteria did work; but there is no way to be certain because there may have been some nitrosomonas still alive in the water. The question arises then, how did they get there in the first place? My guess is from the bottled bacteria, but who knows.

I believe the best way to cycle your system (once you have added some bottled bacteria) is to place your baby fish, be they fry or fingerlings, into the fish tank and begin feeding them small amounts of food. When adding in new fish to your system, you will always be adding in some water from their previous location. This water will contain the bacteria that you need for your Aquaponics system. Slowly increase the amount of food given to your fish while making daily water chemistry measurements. If the ammonia or nitrites gets too high (1.0 ppm), stop feeding your fish until it settles back down to about 0.5 ppm or less. This is just an indication that your fish feeding increase is getting ahead of your bacteria growth.

After about two weeks, you should be able to feed your fish as much as they will eat and not have an ammonia spike. At that time, you can reduce your water measurement frequency to once every few days. You should never go more than a week without making a measurement, however. It is important not to over feed your fish because the excess food will have to be broken down over time by heterotrophic bacteria. In the mean time, your fish water will become cloudy. During this two week cycling process, you should see your nitrates begin to climb. Not to worry, for as I stated earlier, fish can handle higher levels of nitrates than they can ammonia or nitrites by about one hundred to one, depending on the fish species.

Once you see nitrates in your system water, you can start your seedlings in a seedling tray. If the ammonia and nitrite levels are below 0.5 or less, you can then use some of the nutrient rich (nitrate) water from the fish tank to spray the seedlings once they have sprouted. This will help condition them for the transfer into the grow beds where they will receive the full level of the water chemistry in the system. By the time they get transferred into the grow beds, your nitrates should be high enough (10 ppm or higher) to start to support them. As a note, never transfer plants into your grow beds from a soil environment. Soil contains pathogens that can be detrimental to your fish.

Go to Wal Mart and purchase several four ounce bottles of Stress Zyme from the aquarium section for about $4 a bottle. Stress Zyme contains heterotrophic bacteria; and as I mentioned in an earlier post, it will process any left over fish food and fish solid waste. It will also help keep your fish tank water clear. Just follow the instructions on the bottle. We use one bottle a week total in our three 120 gallons fish tanks. It works as advertised. Our fish tank water is relatively clear and there are no fish waste solids over accumulating in the grow beds after 18 months. There will always be some fish solids in your grow beds because it takes time for them to break down. With the addition of the Stress Zyme, we have not seen any continued build up of solids; and we have cleaned our grow beds more than once to remove the excess roots mentioned below.

For your first planting, it is best to plant only green leafy vegetables like lettuce, spinach or basil; as they do not require high levels of nitrates. Green leafy vegetables will grow quite well on 20 to 30 ppm of nitrates. Do not plant tomatoes or other flowering plants the first time out because when they start to flower, they will suck up all of the nitrates from your system. The other plants, along with the flowering ones, will respond by putting their efforts into growing roots in search of nitrates. You will end up with grow beds full of roots and not much happening above (experience speaking here). Wait until your system is considered mature, which is about one year, and your fish have grown out to plant your flowering plants. Even then, go slowly with just one flowering plant per grow bed. Test your water weekly and take special notice of the water measurements when they start to flower. You will need nitrates at or above 40 ppm to support flowering plants, and it will drop considerably when they flower.

At this point you have enough basic information on how an Aquaponics system works, the components necessary to put a working system together and how to start up and operate your system. What I have given you here is just a thumbnail sketch of the complexities of operating an Aquaponics system. If you are serious about becoming an Aquaponics farmer, then I suggest that you join an Aquaponics forum. One such forum can be found at: ” “. This particular forum is for Aquaponics do-it-yourselfers located mainly in the USA. There are, however, members from all over the world on board. There are several other fora located in Australia where Aquaponics has been around for some time. I have learned much from the Aussies about Aquaponics. They use metric units in describing their systems and talk about local fish which are not available here in the USA. Still, much information is to be had from down under because the physics is the same regardless if the fish swim upright or upside down. I just don’t know how they make water run uphill, though.

I hope you have found these posts valuable so far, and I do plan on adding to them from time to time. For now, please consider what you have read and the possibility of becoming an Aquaponics farmer. These posts, up to this point, have given you what you need to start your first system. Keep watching as there is a lot more information coming. Also, please visit our web site for more information, pictures, videos, a live greenhouse web cam and live fish cams with audio.

Best Regards
Oliver Duffy

6 comments on “Aquaponics 101 Part Four: System Start Up

  1. Excellent! I want to start a commercial aquaponics system to raise about 3500 – 5000 (750 – 800g) tilapia per cycle, while growing vegtables such as tomatoes, onions, cabbage, lettuce, and leafy greens. My biggest fear was water testing especially for plant nutrients. Thanks you have given me a starting point on water testing and I think I will be able to further develop from here.
    Thanks for sharing mate keep up the good work.


    • @ Breeza. How is the commericial aquaponics endeavor coming?
      I wanted to also ask; Once one has a system that is mature how do you turn it into a business? Please advise, and thank you


      • So sorry to have missed this question back in August (EGAD!). So far, as is obvious, we’ve been pretty much doing free consultation. Do you have a particular project in mind and where are you located?


      • We have a commercial system idea that we call Aquaponics Earth. You can get to it from Aquaponics USA by clicking on the left side menu (bottom). This is a start up and is in the funding stage. I believe you pretty much have to go into the commercial realm with a system from the beginning. You have to conceive of it and design it to be a commercial system; and it has to be big enough to generate the quantities of fish and veggies necessary to make money. Then you have to have a marketing plan up and running that will get your products into the market place. You need to have a brand and, if you’re going to go the packaging route, packaging. This is where aquaponics enters the business world. It’s a whole concept.


  2. Hi Ruz Lass 4900: Just go to Word Press to start your own Blog. It’s free! And it’s really a fun way to share your passions and ideas with the world. There are other Blog sites that you can explore as well like Blog Spot. To start your own Blog, go to our Blog page and click on Word at the right of our post. That link will take you to the place where you can start creating your own Blog. Have fun and thank you for your interest in Aquaponics USA.

    Sincerely, Grace


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