Aquaponics Explained – Part 2

Welcome back to the aquaponics revolution.

In the last issue we talked about just what aquaponics is (the marriage of aquaculture and hydroponics) and how it works. I described system types and then went into some detail about the creatures that live in a media-based aquaponics system: fish, plants, bacteria, and worms.


This article is the second installment in the two part series. We will now focus on what you need to know in order to build a media-based aquaponics system, including considerations about the fish tank, the grow bed, the plumbing, and the media.  So let’s dive right in.

The size of your fish tank will define the ultimate size and flexibility of your aquaponics system, so consider the tank size early in your design process. If you are building a small, desktop system using an aquarium, you will be restricted to aquarium fish that will live comfortably in the size aquarium you own. If you want to grow larger, edible fish, the most important rule-of-thumb when choosing a tank is to make sure it is made of sturdy, food-grade or food-safe materials. Next, make sure that the tank is at least 18” deep (457mm), and holds at least 50 gallons (189 Liters) of water. Tanks need to hold approximately 50 gallons (189 Liters) or more in order to grow “plate sized” fish (12” and 1 ½ lbs, 300mm and 680g).

Aquaponics fish tanks can be made from just about any structure that has satisfactory dimensions. They needn’t even hold water – just line them with EPDM pond liner. You can also use everything from recycled bathtubs, stock tanks, and IBC tanks, to recycled barrels.

Since you will find it difficult to move your fish tank once you fill it with water, you should carefully consider where you place it. Ideally the fish tank should be located indoors or outdoors in the shade. Fish don’t require sunlight to thrive and the extra heat and algae growth from sunlight can become a problem. Also, be sure the tank is on a solid surface that can handle the weight of the tank when filled with water. At 8.3 pounds per gallon, you will quickly reach a weight that might exceed the structural limits of the surface you are planning to use.

Wherever you choose to set up your tank, you will be well served to at least partially cover it to help prevent debris, children, and pets from falling in. Covering it will also lower the amount of light reaching the tank. This will help you keep control of the tank’s temperature and reduce algae.

Fish tank volume governs the maximize size of your grow bed. Here is why. The plants need the fish waste to thrive. The bigger the grow bed and thus the more plants, the more fish waste required. Simple – you need enough fish to support your plants. In general the recommended grow bed to fish tank ratio is approximately 1:1, i.e. the fish tank volume should be approximately equal to the volume of the grow bed. This ratio can also be thought of in gallons per cubic foot, striving for 6 gallons (22 liters) of fish tank to every cubic foot of grow bed. For example, a 50 gallon (189 liter) tank would be able to support 6 to 8 cubic feet of grow bed. You can extend this rule of thumb all the way to 2:1 (twice the fish tank volume to grow bed volume) but be sure to reduce the stocking density of your fish tank accordingly as this approach reduces your ability to filter the fish tank water with the grow bed plants.

Aquaponics grow beds should be about 12” deep (300 mm). 12” provides enough depth to support most plants and encourages the bacteria and composting red worms in the grow bed to fully establish themselves. A 12” deep bed never needs to be cleaned out because the robust eco-system enabled by a 12” deep grow bed takes care of this for you. Below is an excellent explanation by Australian Murray Hallam of grow bed dynamics – reprinted with permission from his new Aquaponics Secrets video:


Surface or dry zone (Zone 1) – The first 2” (50mm) is the light penetration and dry zone. Evaporation from the bed is minimized by the existence of a dry zone. This dry zone also protects the plant base against collar rot. Additionally, by ensuring that this zone is kept dry, algae is prevented from forming on the surface of the grow bed and moisture related plant diseases such as powdery mildew are minimized.

Root zone (Zone 2) – Most root growth and plant activity will occur in the next zone of approximately 6” – 8” (150 – 200mm). In this zone, during the drain part of the flood and drain cycle, the water drains away completely, allowing for excellent and very efficient delivery of oxygen rich air to the roots, beneficial bacteria, soil microbes, and the resident earth/composting worms.

During the flood part of the cycle, the incoming water distributes moisture, nutrients and incoming solid fish waste particles throughout the growing zone. The worm population does most of its very important work in this zone, breaking down and reducing solid matter and thereby releasing nutrients and minerals to the system. “Worm Tea”, as it is commonly known, will be evenly mixed and distributed during each flood and drain cycle. “Worm Tea” and the fish are entirely compatible.

Solid collection and Mineralization Zone (Zone 3) – This is the bottom 2” (50 mm) of the grow bed. In this zone fish waste solids and worm castings are finally collected.  The solid material has been reduced by up to 60% by volume, by the action of the resident composting worms, and microbial action. During each flood and drain cycle, what is left of the solids percolates down into this zone further and final mineralization occurs in this area via bacterial and worm activity. Due to the excellent action of the flood and drain cycle, this bottom area is kept “fresh” and vital by the excellent delivery of oxygen rich water during the flood cycle.

Warning: Do not use metal containers, not even galvanized metal, for either the grow bed or the fish tank. Metals can quickly corrode, throwing your system off-balance by lowering your tank’s pH. Metal containers may also leach undesirable chemicals into your system. Copper and zinc are particularly dangerous to fish. As with the fish tank, make sure the grow bed you choose is made of sturdy, food-grade or food-safe materials.

The growing media should be inert, meaning that it should not be biologically active or decompose. This enables the best bio-filter for your fish waste and the cleanest system overall. Most aquaponic gardeners use either gravel or expanded clay pellets (e.g. Hydroton).

If you use gravel, it should be ¾” (20mm) to 1” (25mm) in diameter in order to optimize the air exchange within the media for the roots of your plants. Caution: be certain you know where the gravel is from. Many types of gravel, especially granite, can leach lime and other elements, which will adversely affect your pH levels and potentially kill your fish, plants, and bacteria. Marble also tends to increase pH to levels that can quickly be fatal to bacteria, and eventually the fish and plants.

Expanded clay pebbles are more expensive than gravel, but are 50% lighter and more porous so they have optimal gas and water exchanging properties. Best of all, because of their round shape, it’s easy on your hands, roots and stems of your plants – making planting and maintaining your system a pleasure. Plus, you will have no worries as to where it came from! We think it is worth the investment because you will have it for the life of your aquaponic system.

The top 1 – 2” of your grow bed should be left dry to help prevent fungus, gnats, algae problems, and moisture related diseases (see the Dry Zone above).

Flooding the grow bed delivers nutrients to the plants and the bacteria; draining the bed oxygenates the water, the plants roots, and the bacteria. Systems using this method are called flood-and-drain or ebb-and-flow systems, and are what most media-based aquaponic systems employ.

There are three standard flood-and-drain style plumbing systems used in media-based aquaponics: timer based, bell siphons, and flush valve systems.

Timer based systems are the most common and the easiest to install. They are comprised of four components: the water-in pipe, the over-flow drain, a timer, and the pump. To set up a timer-based system you simply attach a pump to a timer and set it to power the pump for 15 minutes every 30 – 45 minutes. While this is much more frequent pump activation than in a traditional hydroponics system it is necessary to provide sufficient oxygen to the fish tank, sufficient filtration for the fish, and sufficient oxygen in the grow bed for all the biological activity (as the water drains from the bed it pulls oxygen behind it through the bed).   Since pythium (root rot) is almost non-existent in aquaponics there is no increased danger of disease because of this increased irrigation frequency. Next place the pump in the fish tank and attach the pump to the water-in pipe that goes into the base of the grow bed. When the pump is activated, water will move from the fish tank into the grow bed until it reaches the level of the overflow drain. The overflow drain should be set to drain at 11” so that the top one inch of the grow bed will be left dry. After 15 minutes of flooding the grow bed, the timer will turn the pump off, allowing water to drain back through the water-in pipe and out through the pump. Though this system is common and easy to install, the downside is that turning the pump on and off can shorten the life of the pump.

bell-siphonIn the bell siphon (AKA auto siphon) system the water pump constantly pumps water from the fish tank into the grow bed. As the water rises, it fills the interior of the bell siphon positioned within the grow bed. When the water reaches the right height, it spills over a pipe within the siphon and creates a low pressure area within the siphon that triggers the siphoning action. The siphon rapidly draws the water from the grow bed into the fish tank until the grow bed is nearly drained, at which point air enters the siphon, the low pressure within the siphon is lost, and the siphoning action stops. Since the pump is always on, the grow bed begins to fill once again and the cycle repeats. This may seem confusing at first, but the bell siphon system can be a great option to explore, as leaving the pump on at all times will increase the longevity of the pump. Plus the extra heat that the pump may generate is actually a benefit to aquaponic systems growing fish that prefer warmer water.  Again, because pythium is so rare in aquaponics the extra heat does not pose an increased risk of disease. There are many excellent videos about the construction of bell siphons available on the internet.

Flush valve systems work very much like a flush toilet. This system requires that a flood tank be added to your fish tank and grow bed setup. The flood tank, being similar to the tank of a toilet, is placed above the grow bed. The grow bed, being similar to a toilet bowl, is placed below the flood tank with the fish tank being the drainage point. Water is constantly pumped from the fish tank into the flood tank. A small siphon collects water that fills a container, which acts as a weight. Once the water is heavy enough it triggers a standard toilet flush valve. This then allows water from the flood tank to drain into the grow beds and then into the fish tanks. The water-filled weight has a hole in it that makes it drain slower than it is being filled, so once the flood tank has emptied the small weight begins to drain. Once the small weight has drained it again is light enough to close the standard toilet valve, re-initiating the cycle.

The pump is the heart of an aquaponics system. When you select a pump, consider a simple rule of thumb – choose one that can, at a minimum, cycle the entire volume of your tank in an hour. If, for example, you have a 100 gallon (375 Liter) tank, than you will want a pump that can pump at least 100 gallons to the height of the grow bed every hour.

It is important to have backup aeration for your aquaponic systems. If your pump fails, your plants will be fine for a day or two but a few hours without moving water could lead to dead fish due to oxygen deprivation.

So now you just put in the fish and the plants, plug in the pump and start growing, right? Not so fast! First you need to establish nitrifying bacteria in your aquaponics system, a process called “cycling”. Without these bacteria, the ammonia the fish produce will not be converted into nitrates, causing the fish to die from ammonia poisoning and the plants to starve from lack of fertilizer.

The key to cycling is patience. To initiate cycling, ammonia must be introduced to attract the naturally occurring nitrosomonas bacteria. After another two weeks, or so, the existence of nitrites will attract nitrobacter bacteria. This second type of bacteria is what will change the nitrites into nitrates. Nitrates are nearly harmless to the fish and are consumed by plants as food, therein filtering the water. After approximately 30 days of cycling, you will reach your goal – low ammonia levels. Now you can fully stock your tank and plant your grow bed. For even faster ways to cycle your system, read on..


There are many ways to introduce ammonia to initiate the cycling process in a fish tank. These are generally broken down into two categories: with fish and fishless cycling. Most people use live fish to introduce the first ammonia to the tank and start the nitrifying process. Since ammonia is poisonous, and there will be no bacteria to convert the ammonia for a few weeks, assume these introductory fish are “sacrificial” and may not survive.

If you choose this route, avoid pet store “feeder fish” since, generally speaking, they tend to already be diseased or near death due to poor conditions. Black skirt tetras, goldfish, zebra danios and barbs are good choices to start cycling your tank. Only feed these first fish once a day during the cycling process.

If you prefer cycling without fish, you can initiate the cycling process by introducing small amounts of pure ammonia (clear ammonia, 100% ammonia or pure ammonia hydroxide), vermicompost, or “humonia” (also known as “pee-ponics” where one urinates into the system to introduce the ammonia).

You can speed up the process by actually introducing the nitrifying bacteria yourself with river or pond water, filters or gravel from an already established tank, or with commercial nitrifying products.

Whether using fish or fishless cycling, it is important to use a test kit to monitor the system daily so that you always know what part of the ammonia cycle the system is in. Be sure to keep the pH between 6 and 8 (at 8 or above the cycling process stops and the ammonia becomes highly toxic) and the water temperature above 50°F/10°C (80°F/27°C is optimal).

Once your ammonia and nitrite levels drop and nitrates begin to appear, it is safe to add plants and fish to your system. If you stick with the recommended fish stocking density (no more than 1 pound per 5 gallons of water), keep your beds fully planted, and follow all the other recommendations in this article, you will find that your grow bed grows better and better with time. Happy gardening!



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