My simple aquaponics system has been relativly trouble-free for about 6 months now. I haven’t had to do anything to it other than feed the fish. (not counting my battle with pH) 
Today, I noticed the drain wasn’t flowing water very well, so I took a look at it and noticed lots of roots had made their way into the holes. I took a piece of all-thread and started hacking the roots away. Then I noticed the grow-bed leaking, so I dug out the drain and took it completely apart. (I was amazed at all the roots in the gravel and how well the roots held the gravel as I dug it out)
The root-cause of my problem was that I poked a hole in the pond liner because the drain was elevated above where it was supposed to be, pulling a pocket of air under the liner, making it vulnerable to my less-than-gentle strikes with a metal object. I think the grow-bed has settled down in the ground over time, and the rigid drain pipe could not move down with it, so it forced the drain up.
The fix was simple, and I should have thought of this when I designed it: Create a flexible joint that will allow the grow-bed and drain pipe to move in different ways without breaking something. I accomplished this with a 12″ piece of vinyl hose and two hose clamps.
I’d like to point out that the debris trap was used while I was cleaning out the gravel. Some pieces made their way down into the drain, and they were safely trapped inside the trap instead of traveling through the long underground pipe.
One other improvement that I’ll make on ‘the next one’ is the big pipe surrounding the drain. Make it big enough to fit your whole hand in. Probably need a 6″ pipe for that, but it is worth it. You need space to get in and clean out the little drain holes on the bottom that are horizontal. The extra space also provides more insurance against roots clogging things up.
