Membrane fouling has become a serious issue in membrane bioreactor (MBR) and may destroy the operation of the wastewater treatment process (WWTP). The goal of this article is to design a data-driven intelligent warning method for warning the future events of membrane fouling in MBR. The main novelties of the proposed method are threefold. First, a soft-computing model, based on the recurrent fuzzy neural network (RFNN), was proposed to identify the real-time values of membrane permeability. Second, a multistep prediction strategy was designed to predict the multiple outputs of membrane permeability accurately by decreasing the error accumulation over the predictive horizon. Third, a warning detection algorithm, using the state comprehensive evaluation (SCE) method, was developed to evaluate the pollution levels of MBR. Finally, the proposed method was inserted into a warning system to complete the predicting and warning missions and further tested in the real plants to evaluate its efficiency and effectiveness. Experimental results have verified the benefits of the proposed method.