The availability of real-time information about the biological activity is a valuable matter in wastewater treatment employing activated sludge processes, and this is represented by the oxygen uptake rate (OUR). In these processes, OUR measurements have been used as a fast indicator of changes in waste load or influx of toxic organic compounds and for monitoring of the process efficiency. In this paper, we propose a method for OUR estimation by using Kalman filters and PWM control of the dissolved oxygen (DO) concentration in the activated sludge reactor. The proposed method presents a shorter response time than the standard online procedure and a lower measurement uncertainty compared to a previous feedback control method, which estimates the OUR from values of the applied control signal and the DO concentration measurements. Simulations are presented to illustrate the method and experiments are performed in a bench scale activated sludge reactor to show the applicability of the proposed estimator in a real system. The results confirm the fast response of the proposed method and its consistency with respect to the standard procedure for OUR computation.