Aquaponics: From Fish to Fertilizer

Aquaponic gardening is the combination of aquaculture (fish farming) and hydroponic gardening. Essentially, an aquaponic system mimics what happens in nature along every waterway present on earth. There are many different life cycles and the nitrification of ammonia from fish waste is just one intriguing strand in the web of ecosystems that make up our world. In nature, waste produced by fish is converted from ammonia to nitrites and nitrates by bacteria. The converted nitrates can then be used by plants as a source of food. In order to produce edible produce and fish, aquaponic gardeners encourage this natural process within their aquaponic systems. By utilizing the fish waste, which was once disposed of by aquaculturists, an aquaponic system can produce an abundance of food in a small area. Proponents of sustainable farming are just some of the people who are ecstatic to discover the possibilities of aquaponics. Hobbyist gardeners are also taking advantage of all the benefits that aquaponic gardening has to offer. A closer look at some of the variables that can make or break a productive aquaponic system will give a horticulturist a better idea of how he or she may be able to incorporate an aquaponic system into his or her garden.

Energy Flow

As we all know, it is impossible to get something out of nothing. The same principle holds true for aquaponics. When examining a complex natural system like aquaponics, it is a good idea to examine the flow of energy and how each stage affects the next. In order for the fish to produce the waste that will be converted into plant food, the fish need an energy source. The main input for any aquaponic system is the fish food. This food is usually high in protein and can be produced in another sub-ecosystem (like a worm bed or cricket farm) or purchased. Once the fish eat and digest the food, waste will be produced. Over 50% of the waste produced by the fish will be in the form of ammonia (fish urine). The remainder of the fish waste, excreted as fish fecal matter, undergoes a process of mineralization. In an aquaponic system, mineralization occurs when heterotrophic bacteria consume the fish fecal matter along with any decaying plant material and uneaten fish food. The specialized bacteria convert all three into ammonia and other compounds. Stepping in next is one of the most important microorganisms existing on our planet: nitrifying bacteria. Nitrifying bacteria live naturally in the soil, water and air and play a vital role in creating nitrates for our world. It is the nitrifying bacteria that convert the ammonia (mineralized by the heterotrophic bacteria or found in fish urine) into first nitrite and then nitrate. Plants consume the nitrate as food thus completing the aquaponic cycle.

When looking at an aquaponic system, it is easy to forget the bacteria that play a vital role in the stability of the system. After all, it’s easy to see the fish and the plants but the microorganisms escape our vision and out of sight is out of mind. However, it is very important to remember that there are really three crops to keep alive in an operational aquaponic system: the bacteria, the fish and the plants.


In an aquaponic system the heterotrophic bacteria and the nitrifying bacteria live on the fish tank walls, organic matter in the system, the growing medium, the pump and the water delivery system. There is usually no need for an aquaponic system to be inoculated with these bacteria as they are all naturally occurring. As soon as ammonia and nitrite are present, these bacteria will show up to do their jobs. When first beginning an aquaponic system ammonia needs to be introduced in order to promote the growth of the imperative bacteria. This is usually done by adding the fish to the system. The fish waste will introduce the ammonia to the system and attract the first of the nitrifying bacteria: nitrosomonas. Nitrosomonas will convert the ammonia into nitrites. Both ammonia and nitrites are toxic to fish but this process is necessary in order to attract the nitrifying bacteria that all aquaponic horticulturists are after: nitrospira. Nitrospira convert the nitrites into nitrates which are generally harmless to fish and are a perfect food for plants. During the cycling process (the start up process of an aquaponic system), the gardener will need to test for the presence of nitrates. Once the presence of nitrates has been detected and the levels of nitrites and ammonia have dropped to a lower level, the system is considered “fully cycled”. At this time, the plants, fish, and bacteria can begin their synergistic livelihoods. Making sure the system’s pH, ammonia, nitrite and nitrate levels are in the desired range is important. In some cases, when one of these parameters is out of the desired range, some corrective action may be necessary. In most cases, the majority of the monitoring for an aquaponic system happens during the cycling process. Once the system has been “fully cycled” and has found balance, much less monitoring is required.


There are many different types of fish that can be used in an aquaponic system. Most fish produce waste in a similar fashion so the only limiting factor is climate and supply availability. Many aquaculturists who have experience with fish farming choose a fish that is quick to mature. In other words, fish that grow quickly and taste good are the best choice if you plan to harvest the fish for food. On the other hand, some hobbyist aquaponic gardeners are more interested in creating the ecosystem and don’t care as much about the type of fish because they are more concerned with the plants and do not plan on eating the fish. For these growers, gold fish, carp, bullhead, catfish, or inexpensive “feeder” fish are all good choices. These types of fish can withstand more variance in temperature and oxygen levels and are relatively easy to maintain. For systems where the fish will be harvested, the most common fish species are tilapia, yellow perch and trout. Tilapia are native to Africa and can easily withstand warmer water temperatures (a common problem for hobbyist aquaponic gardeners). Yellow perch and trout may be a little more finicky but grow quickly and tend to be a more sought after food. Possibly the most important factor to consider when choosing a fish breed is the affect the climate will have on water temperature. It is far more efficient to choose a fish species that will do well in your climate’s average ambient temperature than trying to heat or cool water to meet the needs of the fish. This is especially true for aquaponic systems that will operate year-round. For year-round systems, the average temperatures should be heavily weighed when choosing a fish species so the system can be as efficient as possible. 


There are gardeners who have successfully grown everything from potatoes to fruit trees in aquaponic systems. There is virtually no limit to the plant species that can be grown in an aquaponic system. After choosing the types of plants to grow, they will need to be planted into the system. Planting the plants into an aquaponic system is usually done in one of two ways: directly planting seeds or planting starts. Plant seeds can be planted directly in the medium bed by either sprinkling the seeds on top (good for plants with a shallow recommended planting depth) or by burying the seeds slightly in the medium. With either method, the seeds should germinate quickly and start to grow. Once growing, the seedlings can be treated as they would in any other garden. The rules for thinning out, row spacing, etc. will be similar to that of a soil garden. Gardeners can also plant starts (already established plants) in an aquaponic system. In fact, many gardeners prefer starts because they will immediately feed on more of the nitrates than the smaller seedlings. If planting starts, it is a good idea to thoroughly rinse off all potting soil around the plants’ roots. This will help to avoid introducing any possible contaminates to the aquaponic system.

Types of Hydroponic Systems Used in Aquaponics

Hydroponics is a general term that refers to soilless growing. There are many different types of hydroponic systems; some of which are better suited for aquaponic systems than others. Three hydroponic systems are most commonly used in aquaponic systems. These systems are: media filled beds, NFT (nutrient film technique), and DWC (deep water culture). Before choosing a system, a horticulturist should examine all of the variables that make each system operate smoothly. A close investigation of the particular hydroponic system to incorporate into your aquaponic system will only save time and money in the long run.

Media Filled Beds

Media filled beds are the most commonly used systems for aquaponics. Media filled beds utilize some sort of container or bed that can be filled with the medium (usually rock or expanded clay). Water from the fish tank is then pumped over the medium and the plants grow directly in the medium. The medium also works as a bio-filter over time as it will start to develop an entire ecosystem of beneficial bacteria. Instead of a continuous flow over the medium, a media filled bed can be set up to operate with a timed flooding and draining of the medium. The size of the media bed, the size and type of plants grown and the atmospheric conditions will all play roles in how often the pump is cycled. Aside from its straight forward construction and operation, the biggest advantage to a media filled bed is that virtually any type of plant can be grown.

NFT (Nutrient Film Technique)

NFT is a very common hydroponic growing method but is not as common in aquaponic systems. Water from the fish tank is pumped to a small enclosed gutter or tube where the angle of the tube allows gravity to create a flow of the solution. NFT systems are designed to have only a thin film of nutrient solution at the bottom of the gutter or tube. As the nutrient solution cascades down one or multiple gutters or tubes the plants’ roots, which dangle into the solution, are able to absorb nutrients. In an aquaponic system, NFT is really only suitable for particular crops, like leafy, green vegetables. Larger plants with larger root masses tend to be problematic for NFT systems.

DWC (Deep Water Culture)

Deep water culture for aquaponic systems usually refers to the process of floating the plants on top of the water and allowing the roots to dangle into the solution. Some growers will actually place the plants directly in the same tank as the fish. However, the most successful DWC aquaponic systems usually have a separate tank for the plants where the water has passed through some sort of filter. I have seen growers make filters out of five gallon buckets filled with rock. The rock in the bucket ends up housing millions of beneficial bacteria that help the nitrification process before the water is passed to the tank where the plants are floating.

Where to Place Your Aquaponic System

Location, location, location. The actual location of your aquaponic system is an important thing to consider, especially before filling up a large tank with water (once they’re filled, they’re hard to move). The first thing to be considered is the amount of sunlight the plants will be able to receive. The fish, on the other hand, do not need all that sun. In fact, sun will equate to algae in a fish tank. This is why most commercial aquaponic fish tanks are shaded. Finding a location where the fish tank is properly shaded but the plants still receive enough sunlight is crucial. Some growers will even implement some floating plants in the fish tank to help shade the water from excess sun. Power is another huge consideration. Pumps, heaters, chillers and all those things required for cleaning and maintenance need a power source. Space is another consideration. When first setting up the system, remember that once the plants start growing, they will take up much more room than an empty system.

Aquaponic gardening is a complex but fun way to integrate a living ecosystem into your garden. There is a lot to know about this type of farming before beginning but that does not mean you should be intimidated. Aquaponics give rural and urban gardeners the opportunity to produce a large amount of food in a relatively small space. On top of that, it allows them to do so in a sustainable manner. Using the waste product of one resource to fuel another is one way we can make our world better. Aquaponics gives commercial growers and hobbyists alike the ability to experiment with the future of horticultural sustainability.

Eric Hopper is the MyGardenAndGreenhouse.com editor.

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