This paper presents a new software developed in MATLAB for analyzing on-line data of an aerobic SBR, detecting faults and, in this case, proposing the most probable causes of fault. Process diagnosis is achieved using a statistical method divided in two main phases: off-line model building and on-line data diagnosis. The off-line model identifies the correct working conditions of the system (standard operative conditions). It includes the characterization of the deviation of the system from these standard conditions in the case of changing in the biomass properties or carbon and nitrogen load characteristics. The on-line diagnosis aims at collecting and analyzing all the available data available through industrial sensors, and at classifying the behavior of each treatment cycle. The diagnosis performance of the proposed method is tested using a data set of an aerobic SBR pilot plant.