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I have a small system with a concrete mixing tub as a bed that has a bell siphon that runs into another concrete mixing tub that is working as a raft.  

I figured the media bed would filter out the solids but I just picked up the raft and looked inside and I saw a pile of about 2 inches high of fish poo.  

And the roots look like this:

Any ideas on how I could add another filter where the bell siphon exits?  So I could remove even more of the solids?  

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How about a settling tank? You could have your bell siphon empty into that and then have it run into your raft tank.

Do you have any links? or pics of a settling tank from a bell siphon?

How many fish do you have? How much are you feeding? That looks like a lot of fish poop. Maybe try a deeper media bed and also a swirl filter that drains into your media then have your media bed drain into your raft.

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