Display omitted •A control system for the continuous flow operation of solar photo-Fenton was designed.•Two micropollutant removal targets were evaluated: 70% and 90%.•Disturbance rejection was successfully achieved.•Cost efficiency improvements from 45 to 50% were achieved.•Water treatment capacity was studied over different seasons of the year. This work presents a control approach for the continuous flow operation of the solar photo-Fenton process in raceway pond reactors designed for micropollutant (MP) removal from urban wastewater treatment plant secondary effluents. The control system was designed using the mechanistic and semiempirical kinetic model of the photo-Fenton process at acidic pH developed and validated in previous work. Afterwards, a simulation study to demonstrate the viability of the control system was conducted under different operating conditions (hydraulic residence time and liquid depth) for solar irradiance and water temperature variation over the year. Two liquid depths (10 and 20 cm) and two hydraulic residence times (15 and 30 min) were selected as operating conditions to study the system performance for different MP removal control setpoints (70 % and 90 %). For 90 % MP removal setpoint, cost efficiency reductions of up to 21 % were reached, which denotes that the process efficiency is significantly influenced by the control setpoint. This is because highly demanding MP removal setpoints are achieved through high non-linear reagent consumption, resulting in low operating cost efficiencies of the process. On the other hand, cost efficiency improvements from 45 to 50 % were achieved when an 70 % MP removal setpoint was adopted, when comparing the manual operation of the process with the automatic mode. The presented results demonstrate not only the feasibility of implementing an automatic approach for the solar photo-Fenton process, but also the need for an optimised, efficient and controlled operation to upgrade its competitiveness versus conventional technologies.