The aim of this work is to study the effects of six operational variables, i.e., dissolved oxygen (DO), nitrate recirculation flow, sludge recycle flow, sludge wastage flow, external carbon dosage, and anoxic volume fraction, on the performance of nitrogen removal and its control in a pre-denitrification plant. The results obtained show that the six operational variables have a significant influence on nitrogen removal in such a system, while the utilization of the control strategies can improve the situation to a significant extent. The control of DO concentration should be correlated with the influent ammonia load, the effluent requirement and nitrification type. The anoxic effluent nitrate concentration should be controlled at ca. 2 mg/L or the ORP value at the end of the anoxic zone should be controlled at ca. -90 mV. The control of the sludge recycling flow by online monitoring of the sludge blanket height (SBH), is an alternative to the conventional control of the constant sludge recycle flow. It may be possible to achieve the automatic control of sludge wastage flow by online measuring of the ammonia concentration and the nitrification capacity of the sludge. The recirculation of nitrate and external carbon dosage should be simultaneously controlled to optimize nitrogen removal. The anoxic volume fraction should also be optimized, to ensure a good balance between nitrification and denitrification.