The application of near infrared (NIR) spectroscopy for industrial process monitoring is achieving increasing importance over the last twenty years. In fact, the real time monitoring capacity of NIR spectroscopy is a very important feature for process monitoring, prediction and control as it allows a fast evaluation of the state of the process. However, the application of NIR spectroscopy in wastewater treatment processes is still to be explored. Although some applications of the technique for wastewater monitoring have been reported in the literature, there is still a need for more investigation related with applications, limitations and advantages of the technique when compared with other methods. An activated sludge reactor for aerobic treatment of a complex medium was monitored in situ with a NIR transflectance probe and traditional chemical parameters analysed off-line. NIR spectrophotometric data measured at the feed, reactor and settler were coupled to principal component analysis (PCA) to infer about the ability of this monitoring system to detect changes in the feed influent. The analysis of the score plots resulting from PCA permitted to identify the moments at which the perturbations occurred and to follow the consequent instability induced in the reactor till the day where the system is recuperated. The promising results obtained, suggest the interest in more detailed studies on the feasibility of NIR spectroscopy as an alternative method for monitoring and control of wastewater treatment processes.