Aquaponic Gardening

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My plants are not thriving... question about stagnation?

I am having trouble with poor progress of my garden. I have a continuous flow in a 30 gallon Rubbermaid bin. My plants are affixed in expanded clay pellets that float on top of the water. I had my in-feed tube just stuck in the garden bed under the clay layer.
The water trickles in and flows out through a drain pipe that is as high as the water level that the clay floats on.

I initially had a flood and drain system with an automated siphon, but the clay shifted violently. I removed the siphon and kept the system as it is now.
I suspect that my problem is stagnation in the garden bed reservoir.
What if I put in an aeration stone?
Would that oxygenate the water and move it around sufficiently?

Also, I moved the in-feed tube above the clay, on the surface, so that the nutrients can flow over the roots, presumably.

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