I agree with Alexandros. I would not change conditions throughout most of the bed; leave them anaerobic. But you need to increase the oxygen availability in a zone near the outflow (or perhaps add a new short treatment zone that is dominated by aerobic conditions). The roots of living wetland plants would be one way to do this.

Thank you Alexandros stefanakis and John Nyman.

@John Nyman : In your reply, you mentioned about roots of wetland plants would be one way to do this. Can you provide more details regarding the same?

@Alexandros stefanakis: Does HRT of 36 hrs and temperature of less than 20 degree Celsius would affect increase in outlet ammonia concentration?

I don't know for the retention time, but temperature about 22 degree is kind of optimal, below 16 degree is not favorable, below 5 is crucial.

Lowering the temperature will inhibit nitrification/denitrification, which removes nitrogen from the system; thus ammonia concentrations will increase as degradation of organic matter continues. Nitrifying bacteria require free oxygen as well as substrates within the water column. Thus, reducing floating or emergent macrophytes in the treatment cell could inhibit nitrification, causing effluent ammonia to increase.