This paper presents the real-time control strategies developed to regulate both the ammonia and nitrate concentration in the effluent of the new Vitoria WWTP (Spain). Nitrate control aims at the optimal use of the denitrification potential at any moment. For this purpose, the proposed control algorithm continuously adapts the internal recycle flow in order to maintain a desired nitrate set-point in the anoxic zone. Ammonia control aims at maintaining the required average concentration of ammonia in the effluent by manipulating the Dissolved Oxygen (DO) set-point. The control strategies have been based on a hierarchical structure where a high-level or supervisory control selects the set-point of the low-level or conventional controllers. The design of the controllers was carried out using the Quantitative Feedback Theory QFT for the design of robust control systems. Moving average values of some variables have been introduced in order to eliminate the perturbations associated with the daily 24-hour profiles. The controllers have been verified using long-time dynamic simulations based on a mathematical model previously calibrated in pilot plant. Influent load and temperature used in the simulations correspond to the real values measured in the full-scale WWTP during 12 months. The results obtained in the simulations show the good performance and stability of the control strategies independently from external disturbances. A short-time experimental verification of the controllers in pilot plant with real wastewater is also presented.