In this paper, a novel application of state estimation in environmental engineering is presented. Filtering techniques including moving horizon estimator (MHE) and extended Kalman filter (EKF) are used for early concentration estimation of toxic agents existing in water supply. The purpose is to integrate the filtering techniques with an early warning system enabling an early detection of the presence of toxicants in the water supply system and quantifying their concentrations. The estimation is based on dynamic measurements generated by a real-time cell electronic sensor (RT-CES) and cytotoxicity dynamic models.