The methods behind the predefined impulse response function in continuous time (PIRFICT) time series model are extended to cover more complex situations where multiple stresses influence ground water head fluctuations simultaneously. In comparison to autoregressive moving average (ARMA) time series models, the PIRFICT model is optimized for use on hydrologic problems. The objective of the paper is twofold. First, an approach is presented for handling multiple stresses in the model. Each stress has a specific parametric impulse response function. Appropriate impulse response functions for other stresses than precipitation are derived from analytical solutions of elementary hydrogeological problems. Furthermore, different stresses do not need to be connected in parallel in the model, as is the standard procedure in ARMA models. Second, general procedures are presented for modeling and interpretation of the results. The multiple-input PIRFICT model is applied to two real cases. In the first one, it is shown that this model can effectively decompose series of ground water head fluctuations into partial series, each representing the influence of an individual stress. The second application handles multiple observation wells. It is shown that elementary physical knowledge and the spatial coherence in the results of multiple wells in an area may be used to interpret and check the plausibility of the results. The methods presented can be used regardless of the hydrogeological setting. They are implemented in a computer package named Menyanthes (www.menyanthes.nl).