The combined SHARON-Anammox process is a promising technique for nitrogen removal from wastewater streams with high ammonium concentrations. It is typically applied to sludge digestion reject water, in order to relieve the activated sludge tanks, to which this stream is typically recycled. This contribution assesses the impact of the applied control strategy in the SHARON-reactor, both on the effluent quality of the subsequent Anammox reactor as well as on the plant-wide level by means of an operating cost index. Moreover, it is investigated to which extent the usefulness of a certain control strategy depends on the reactor design (volume). A simulation study is carried out using the plant-wide Benchmark Simulation Model no. 2 (BSM2), extended with the SHARON and Anammox processes. The results reveal a discrepancy between optimizing the reject water treatment performance and minimizing plant-wide operating costs.