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In wastewater treatment plants (WWTPs) management the need to meet the increasingly stringent quality standards and at the same time to minimize the operational costs has prompted the development of efficient fault detection and isolation (FDI) methods to backup the existing control systems. The aim of this paper is to develop a new fault detection (FDI) algorithm for alternate aerobic\anoxic cycle waste-water processes for nitrogen removal. The proposed FDI algorithm is based on an adaptive version of the principal component analysis (PCA) and monitors the data produced by the ammonia and nitrate probes deployed in the oxidation tank. The adaptation of the reference system is required by the time-varying nature of the WWTP processes and is achieved by means of a moving window updating system.