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Reliable temporal modelling of groundwater level is significant for efficient water resources management in hydrological basins and for the prevention of possible desertification effects. In this work we propose a stochastic method of temporal monitoring and prediction that can incorporate auxiliary information. More specifically, we model the temporal (mean annual and biannual) variation of groundwater level by means of a discrete time autoregressive exogenous variable (ARX) model. The ARX model parameters and its predictions are estimated by means of the Kalman filter adaptation algorithm (KFAA) which, to our knowledge, is applied for the first time in hydrology. KFAA is suitable for sparsely monitored basins that do not allow for an independent estimation of the ARX model parameters. We apply KFAA to time series of groundwater level values from the Mires basin in the island of Crete. In addition to precipitation measurements, we use pumping data as exogenous variables. We calibrate the ARX model based on the groundwater level for the years 1981 to 2006 and use it to predict the mean annual and biannual groundwater level for recent years (2007-2010). The predictions are validated with the available annual averages reported by the local authorities.