A system identification approach can be incorporated in groundwater time series analysis, revealing information concerning the local hydrogeological situation. The aim of this work was to analyse water table fluctuations in an outcrop area of the Guarani Aquifer System (GAS) in Brotas/SP, Brazil, using data from a groundwater monitoring network. The water table dynamic was modelled using continuous time series models that reference the hydrogeological system upon which they operate. The model's climatological inputs of precipitation and evapotranspiration generate impulse response (IR) functions with parameters that can be related to the physical conditions concerning the hydrological processes involved. The interpretation of the model parameters from two sets of monitoring wells selected at different land-use sites is presented, exemplifying the effect of different water table depths and the distance to the nearest drainage location. Systematic trends of water table depths were also identified from model parameters at specific periods and related to plant development, crop harvest and land-use changes.