One issue I can think of is you wouldnt want the roots submerged in water all the time in the top portion. The aquaponic setups I've seen have a basin below with a pump that fills the plant basin periodically, but then the water slowly drains out. Otherwise, your terrestrial plants or veggies roots will just rot away. If you are thinking semi aquatic plants, different story. I'm not sure how it would work out if you wanted a continuous flow throughout the whole system.

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