Hey, Aggie. This seems to be a common problem with this kind of setup. It isn't so much the fish poo, it is the dirt that is pushed out of the pots by the roots. You need a filter to trap the stuff thats in the water.Some people put filter material around the pump and don't realize the dirt just migrates back into the water.

Easy way to add a filter as Sleepless said is fill a mesh bag (like onions come in or a mesh bag for delicate laundry) with quilt batting. Your pump should be nestled in the middle - you'll probably have to cut a small hole for the cord. You'll need to rinse out or replace the quilt batting often at first (like daily if its really dirty), but as the water clears - less often.

Also, if you are changing out 1/3 of the water, try to syphon it out of the bottom, removing more gunk.

Good luck! S