Aquaponics systems use one of two water recirculation systems primarily. One method is the "flood system", "flow system", or "constant flow" system. This system runs the water continuously through the root systems of vegetables. The other method is the "flood and drain" or "ebb and flow" system. This system adds water to grow beds causing the water level to rise to just below the media surface, and then drains the water and repeats the process continuously.
Flow systems are good for salad green farming. Flood and Drain systems are good for all types of vegetables but are a little more complex.
As you have seen from my setup schematic, http://wolfenhawke.blogspot.com/2012/10/single-pump-aquaponics-system-design.html, I use Flood and Drain in my system. This is accomplished by using a bell siphon in the grow bed. This apparatus does not use energy but counts on vacuum created in a sealed water system. There is plenty of information on building your bell siphon. One paper is available here, http://www.ctahr.hawaii.edu/oc/freepubs/pdf/BIO-10.pdf.
Since my grow beds had a drain plug on the side, I used this. I do not recommend going from the side as the setup is more complex to tune, but I am showing this for interest/information. Certainly, you can setup your similar beds with the draining straight down.
As you can see, my internal standpipe makes a 90 degree bend which is non-standard.
After that the bell pipe is installed on the standpipe. Note, one disadvantage with the 90 degree standpipe connection, is that the bell pipe cannot seal as far to the bottom. The top of the cut at the bottom of the bell pipe determines the minimum level of water in the grow bed. My bed will have about two inches of water always at the bottom.
After this stage, you can fill the planter with your media. As you can see, one benefit I do have with the 90 degree install, is that I can tune the height of the water draining by turning the bell pipe and standpipe as a unit. I had to do this on all my planters to get the desired height -- this is likely because I do not use "snorkels" on my bell pipe and the trapped air is compressing and affecting the rising water level.
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