Ammonia levels can be a ...

Ammonia levels can be a problem, which can be dealt with using a fully aerated system and ensuring that live ammonia-oxidising bacteria are present.  As Eros Kaw rightly said, it is the materials, which inhibit bacteria such as phenolics that cause problems.  There are bacteria adapted to the growth on these materials.  It is one of the places where membrane technology can be useful.  The reed beds can also be used as a polishing system but may not be the best at removing high levels of hazardous materials.