Aquaponic Gardening

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There has been a gradual build up on a brownish substance inside the gravity drain pipe from my fish tank to the sump pump.  I noticed today that the water level in my fish tank was starting to rise. I removed the drain pipe to discover the nylon filter I installed over the drain cap to keep out the little fish (the inlet is near the bottom of the tank) was nearly clogged with very fine brown 'gunk.'  It was impeding the flow of water out of the fish tank. Unattended it could have clogged the drain and let the tank overflow.  

In the process of removing the pipe from the tank (I never glued it so it could be removed if needed) I found the pipe coated with the material, as was the drain pipe outside the tank.  

Am I right in assuming that this could be either algae, fish waste or both?  I washed out the pipes in the sump tank so the material would remain in the system, assuming it will be good for the plants and bio-filter bacteria.

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you are right, it's fish waste - and vital to your system. Good move on rinsing in the sump tank aswell. rinsing in tap water would have flushed nutriemts down the drain & would have killedoff any bacteria growing on the pipe/nylon (chlorine)

Gunk.  Likely a combination of bio-slime, fish poo, uneaten feed, perhaps some algae.  Fine screens always need more frequent cleaning than a coarser screen or Grate.  In any tank I have with larger fish, I swap to a grate or net pot over the drainpipe to allow the water and stuff to flow through easier with less clogging.

This slime build up is the main reason that many of us don't use smaller pipes since in a big system or heavily stocked system the slime can build up to the point of really impeding the flow of small pipes.

Well, I am experiencing the exactly same thing. From reading some of the comments here, does it mean I have to replace my piping system to a bigger one? That's gonna be a bummer... I mean, is there something we could use (something like chlorine) that would not harm the fish and the vegetables

If your piping is too small, your piping is too small for a bio-ponic system.  If you were to use something like chlorine or anything that would stop the bio-slime, you would be killing the whole system so what would be the point, you might as well do sterile hydroponics in that case.

Use bigger pipes.

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