Sweet post! I've been debating with myself about setting up an aquaponic system on my roof, albeit a smaller one. There are a lot of issues to consider, and water is a major one. Also, the question as to which water to use? Tap-water or rain? Here in Mexico City each one has its own drawback. Sure the chlorine can evaporate, but the pipes supposedly carry all sort of other stuff, but so does the rain, once it has fallen through the smog layer. For my plants, my worms, and my spirulina I've been using both, and they seem to be thriving in any case, but I don't know if an aquaponic system would be less resilient.
Of course a possible solution would be a solar distiller... yet more infrastructure to build.
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