Short-term prediction of hydrological time series using chaotic dynamical systems approach has gained popularity. However, noise can severely affect the prediction accuracy of any data driven modelling approach. Noise reduction processes attempted in chaotic hydrological time series analysis were later questioned by Elshorbagy et al. (2002) for their appropriateness for noise reduction processes. Only a few studies on noise reduction have appeared since then, and these too were limited to introducing new noise reduction methods.Most of the past studies on chaotic time series noise reduction shared a general perception that the noise reduced data trained models can give better predictions; they used off line noise reduction methods to obtain a ‘noise reduced data set’ which was then used to make prediction models. However, the results of this study showed that this was not necessarily true and often flawed, when the input data was noisier. Instead, noise-reduced data inputs, were shown to yield higher prediction accuracy even with noisy data trained models. Thus, the study showed a real need to use real-time noise reduction methods instead of off-line noise reduction methods that had previously been used.The Extended Kalman Filter (EKF), a popular nonlinear state estimation method from controls literature, was introduced as a real-time noise reduction method and its effectiveness was demonstrated on both synthetic chaotic time series and real river flow time series. EKF produced prediction improvement as high as 15%–40% on the benchmark time series with noise levels varying from 1% to 30%. Two river flow series, with low average flows, showed prediction improvement whereas three other flow series, with relatively large average flows, did not. Artificial Neural Network (ANN) models were used as the state-space models in EKF, and adopting them to time delays different from 1 unit was also demonstrated. The study demonstrated an ‘indirect’ validation method to verify the effectiveness of noise reduction when several interrelated time series were available; this was supported in observed discharge time series of the Ciliwung River in Jakarta, Indonesia.