Aquaponics USA

Aquaponics 101 Part 4


Aquaponics 101

Part 4

"Congratulations, you've made it to Part 4 of Aquaponics 101. Assuming you've gone through Parts 1-3, you now have the know how to build an efficient, reliable AP System.

The next step is called System Start Up, Operation and Maintenance. This info comes in two Parts, Part 4 & Part 5."


Aquaponics 101 Part Four: System Start Up, Operation & Maintenance:

This is the fourth in a series of Tutorials that are going to teach you much of what you need to know about Aquaponics.

In Part 1, “The Bio-Chemical 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). Aquaponics allows you to grow food for yourself and your family year- round as long as your AP system is in the proper environment. I also gave a description of the bio-chemical processes involved that make Aquaponics work.

In Parts 2 and 3, “System Design”, 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 AP component called the grow bed, which is the most important part of an AP 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 Start Up, Operate and Maintain your system, but first we need to talk about water. To your AP 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 (DO). As mentioned earlier, an AP system with ample DO 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 or milligrams per liter). The only way to know the value of DO in your system is to measure it, and the best way to do that is to have a DO meter. The design guidelines I have given you in the previous parts will assure that you achieve this goal, so the actual purchase of a DO meter is desirable but not crucial.

Most backyard Aquaponics hobbyists don't pay much attention to DO levels because in the past the DO meter was rather expensive. They are investing minimal money into their systems, and the price of a DO meter is not in their AP 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 them was more than I could stand. We now have available a high quality Milwaukee Instruments Dissolved Oxygen Meter at an affordable price.


As I wrote in Part 1, 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. Above are three photos of plants growing in our Greenhouse. Although the corn grew beautifully, we don't recommend growing it in a Greenhouse unless the roof is extra tall because once our corn hit the roof, it couldn't produce it's fruit. The only stalk that did produce a delicious ear of corn was the one that was able to grow out of our sky vent to it's full size at which point it fruited.

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. Each number is ten times the next lower number and one tenth the next higher number. So, a change of one number on the pH scale is a change of ten times. 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 7 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 as it is absorbed by the alkaline buffers. You can keep adding acid to your water until you have saturated the alkaline buffers, but understand that acid + alkaline convert to salt + water. What this says is that what you will end up with is a more neutral pH and salty water.

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 with buffers before the bacteria started doing their job. As the fish grow out, and you feed them more food, they will produce more waste causing the bacteria to 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. This will also increase your total dissolved solids (TDS) in the form of salt, mentioned above. 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 if they are in your water, because they do not evaporate with the water.


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 AP system.

We have found that a pH of 7.3 from our 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 to off-gas (evaporate) out of the water before transferring it to the fish tank. Because adding water is a repetitive chore for an AP farmer, this separate tank method becomes a hassle after a while. Adding a catalytic 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 too 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. Monitoring your pH with a pH meter is very simple and requires less than a few minutes to make an accurate pH measurement. 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.

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 water temperature and give an accurate reading. This allows me to see the slightest change and gives me a warning if something is out of the ordinary. You should never let your pH meter probe dry out. Letting it dry out will cost you another probe, for they cease to function once they have become dry. I calibrate the probe using calibration solution and adjust it to a pH of 7.0 on a weekly basis.

I do not recommend adding pH up or pH down chemicals to your fish tank water, unless they contain only Potassium Hydroxide. Many off-the-shelf pH up solutions contain elements that are not friendly to either plants or humans. Remember, this is an AP 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 AP 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, the beneficial bacteria and the plants.

You can also use Calcium Hydroxide (Lime) as a pH-up. It is important to mix it with lots of water prior to adding to your system and even then, go slow–very slow. Make certain that whatever you use is pure and doesn't have any other chemicals added, as it can kill your fish.

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. We offer Hydroton with shipping from our supplier's nearest-to-you warehouse, thereby reducing the shipping price. Once it is shipped to you, any shipping overcharge will be refunded. Buying larger quantities will both reduce the purchase price and the shipping charges. Hydroton is a one-time purchase as you can use it over and over.

Some Aquaponics do-it-yourselfers go down to the local river, gravel pit or Home Depot 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.

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 Fº range. You can see the water temperature conflict.



A Float Valve will assure you that the water in your Fish Tank remains at the proper level. Your water will never get too low to stress or worse, kill your fish. With proper installation, it will automatically fill your tank as needed.

Every time-saving device you can add to your AP System is a real help. This inexpensive gadget is great.

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 AP farmer, I would not recommend raising Trout. You might want to consider Carp if you don't plan on eating your fish, although some people eat Carp. Look into the fish species that is best for your climate and legal for your area.

Once your system is assembled and the grow beds are 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. You might want to consider some kind of a power back-up in case of a power failure.

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. There are differing opinions as to how to accomplish this task. There are commercial products like API Quick Start pictured above that claim to contain living bacteria; and we have used this and provide it with our systems. However, I make no claim of its viability. Another source of this starter bacteria is your (or a friend's) aquarium water. You can take some of it and place it in your AP fish 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. Upon receiving your fish, they will be in water that contain bacteria. So, that may suffice if you do not use fishless cycling (below); in which case you will need some starter bacteria.

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 fishless cycling 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 non-prescription drugs) that you do not want in your AP system. Remember, we hope you are planning on growing organic fish and veggies in your system, so keep it pure and your fish alive. This whole process is known as "fish-less cycling".

In starting our first system, we added some of the bottled bacteria I mentioned above. We then added some diluted pure ammonia. Later we added too much ammonia and killed off the bacteria that convert nitrites into nitrates. We knew this because we had very high levels of nitrites and zero nitrates. So, we exchanged some water and added more bottled bacteria and everything started to work.

Quick Start has served us well; and we provide it with all the AP Systems we sell. So far all of our Home & School clients have found that it works great for cycling their systems and bringing in the needed beneficial bacteria for the system to work.

The bacteria are the invisible third living organism after fish and plants that you need to be growing in your AP System. Without them, your system is quite literally dead in the water.

You will never see your bacteria; but you will know if they aren't doing well because your system chemistry will show you. Your Nitrate numbers will plummet and your Nitrite numbers will go up.

That's the sign that your bacteria are in trouble; and you'll need to add more Quick Start, which acts like food for the bacteria. They multiply once they are properly fed.


A pH Meter is a must have if you want to keep your fish alive and well. We've discovered that pH can fluctuate over time for a variety of reasons so it needs to be measured frequently.

The unit comes complete with probe,  nine-volt battery, and 20-mL sachet of calibration solution. It's easy to calibrate and use.

To Go Directly to Part 5, Click Here

Or get a piece of paper & a pen and take the Part 4 Knowledge Quiz below:

To Go to Part 5, Click Here

Congratulations! You've just completed Aquaponics 101, Part 4.

Now it's time to test your knowledge. Take the Part 4 Quiz here:

1.  What element besides DO in your AP System provides life to

    the organisms in your system?

2.  The best way to measure the DO in your system is to use

    a ___________.

3.  What does the "p" stand for in the symbol "pH"?

4.  What does the "H" stand for in the symbol "pH"?

5.  When pH is neutral, it is at what number?

6.  If you add acid to your water, your pH goes (up or down).

7.  What is the function of a Float Valve in an AP fish tank?

8.  What is the purpose of an API Freshwater Master test Kit?

9.  What items does the Fresh Water Test Kit measure?

10. To measure pH, it is best to use a __________.

11. Where do you place your pH probe when it's not in use?

12. If you use a commercial pH-up solution, it is safe it contains

    only ____________.

13. Calcium Hydroxide (Lime) can also be used as a

    ____________ solution as long as you use it sparingly.

14. Why does gravel from a riverbed or supplier sometimes

    cause a problem in your AP System?

15. What does Cycling Your System mean?

Part 4 contains a lot of information about the water in your System. To quote Oliver, "To your AP System, Water is Life". He goes on to discuss the important things that need to be measured in your Water like the Dissolved Oxygen Level (DO), the pH Level, the Total Dissolved Solids (TDS). Once the water is right, it's time to Start Up your System and start Operating and Maintaining it, which is all explained below.

Aquaponics 101 Part 4