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In this article, we use a transfer function-noise (TFN) modelling strategy with single output and multiple/single inputs to study the relationships among a large unconfined aquifer in the upper Venetian plain (Northeast Italy), its recharge components (rainfalls and losing river) and a multi-layered confined system located in the middle Venetian plain. Model identification from the data raises a range of difficulties when seeking models with consistent physical behaviour, but no information related to the transfer function order and the lags with no zero weights is available. Therefore we use an automatic identification procedure for TFN models. The obtained results suggest that the rainfall component is more important than the river discharge in the unconfined aquifer, and the behaviours of the deep-confined aquifers are synchronous with that observed in the Badoere area. Copyright © 2010 John Wiley & Sons, Ltd.