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Aquaponics growing pains

 
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Hey guys so the wife and I kinda jumped head first int aquaponics. We just got it all plumed up and I’ve been testing the siphon system.
Well had a mishap and lost 10 gallons of water from a leaky tank overflow 🙈 dumb on my part didn’t thread tape a seal and lost suction. Wife was not happy lol.
Moved on from that and now noticed that my grow bed doesn’t  drain completely. There 2 feet wide by 4 long, and 1 foot high. There filled with lava rock. Tracked it down to my bell portion of the siphon sitting on top of my bulkhead fitting. This prevents me from draining the last 3 inches from the system. Is this a problem? Can you have water in the bottom of the grow bed all the time?
I’m currently looking for something to use that’s a hair bigger to allow the bell to fit over the bulkhead fitting and thus allow the siphon to drain lower, the problem being I need something about 2 1/2 inches wide and we don’t have that for pvc at the hardware stores near me. 3 inch might work,so I’m going to look at that but I think it will be to tight in the 4 inch pipe I have as my walls to hold the lava rock out.
https://worldwaterreserve.com/wp-content/uploads/2018/10/bellsiphon.jpg
For those who don’t know what a bell siphon is here’s a link
Having learned about these I now think they could be really useful for lots of things.
 
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