Although often perceived as tools for use by scientists, mathematical modelling and simulation become indispensable when control engineers have to design controllers for real-life wastewater treatment plants (WWTPs). Nonetheless, the design of effective controllers in the wastewater domain using simulations requires effects, such as the nonlinearity of actuators, the time response of sensors, plant model uncertainties, etc. to have been reproduced beforehand. Otherwise, control solutions verified by simulation can completely underperform under real conditions. This study demonstrates that, when all the above effects are included at the outset, a systematic use of simulations guarantees high quality controllers in a relatively short period of time. The above is exemplified through the Mekolalde WWTP, where a comprehensive simulation study was conducted in order to develop a control product for nitrogen removal. Since its activation in May 2011, the designed controller has been permanently working in the plant which, from this time onwards, has experienced significant improvements in the quality of water discharges combined with a lower utilization of electricity for wastewater treatment.