A two year pilot plant study has been performed in order to evaluate a nitrifying trickling filter (NTF) process within an upgrading project for increased nutrient removal. The operation of the filters was very stable without upsets due to predators. The filter microfauna was dominated by worms and the presence of filter fly larvae was limited. Suggested predator control methods like flooding or varying the flushing intensity did not affect the identified microfauna. By operating the filters in a two stage alternating series filtration mode, higher nitrification rates and lower effluent ammonia concentrations could be reached simultaneously in comparison to operating the filters in a single stage filtration mode.