In this paper, a robust state estimation method based on a filtered high-gain observer is developed for the alternating activated sludge process (AASP) considered as a nonlinear hybrid system. Indeed, we assume that the biodegradable substrate and the ammonia concentrations in the AASP model are unmeasured due to the high cost of their sensors whose maintenance is also very expensive. The observer design is based on the association of the classical high-gain observer and the idea of the application of linear filters on the observation error to deal with measurement noise. It is shown through a Lyapunov analysis that the designed observer ensures the estimation of the unmeasured states (the biodegradable substrate and the ammonia concentrations) based on the measured dissolved oxygen and nitrate concentrations subject to noise. A comparison with the classical high-gain observer is performed via numerical simulations in order to show the robustness of the suggested estimation approach against Gaussian measurement noise.