A systematic design of an optimal control structure for the SHARON-Anammox nitrogen removal process is studied. The methodology incorporates two novel features to assess the controllability of the design variables candidate for the regulatory control layer: (i)H-infinity control method, which formulates the control problem as a mathematical optimization problem, and (ii) close-loop disturbance gain (CLDG) plots. It is shown that the methodology is especially appropriate for bioreactors. The solution of the mixed sensitivity stacked He, control problem ranked the combinations of controlled variables (CVs). The best candidates to CVs were paired with the manipulated variables using the relative gain array. The proposed control structure was further analyzed and verified for disturbance rejection using the CLDG plots. The optimal pairing of CVs with the actuators (k(L)a and acid/base addition) is found to be dissolved oxygen (DO) and pH in the SHARON reactor. Furthermore, to relate the controller actions to process operation objective, nitrogen removal efficiency, two cascade control systems are designed. The first cascade loop controls TNN/TAN ratio in the influent to the Anammox reactor by adjusting the set point for DO in the regulatory layer, while the second cascade loop controls the nitrogen removal efficiency (i.e. effluent TNN and TAN) by adjusting the TNN/TAN ratio at the effluent of the SHARON reactor. The control system is evaluated and benchmarked using a set of realistic dynamic scenario simulations, demonstrating that the different control strategies successfully maintain stable and high nitrogen removal efficiency. The nested cascade control structure shows the hest performance, removing up to 95% of the influent ammonia. Both the control design methodology and the resulting optimal control structures are expected to contribute to stable operation and control of these emerging nitrogen removal technologies. (C) 2015 Elsevier Ltd. All rights reserved.