This paper presents a novel real-time control and electronic instrumentation system (RTC\andEIS) for a prototype plant that uses activated sludge for wastewater treatment. The main contribution in this research was oriented to work on an experimental design with small dimensions and low cost. This design was carried out using two continuous flow storage tanks in which an identification process was carried out with the MATLAB system identification toolbox to know a mathematical model. The mathematical representation obtained is presented as a continuous and a discrete transfer function. To evaluate the performance of the temperature control and instrumentation system, we implemented a simulation of the closed-loop control system and then implemented it using a DAQ, LabVIEW software, electronic devices and the wastewater treatment plant prototype to compare both results. Finally, the secondary treatment effluent was analyzed in a certified water laboratory to have a detailed analysis compared to the initial influent.