A lumped water balance model was used to derive a monthly water storage series in the Salado–Juramento southern basin, for the period 1954–1986. The evapotranspiration term was estimated using the Bouchet's complementary relationship. Different evapotranspiration formulas following the concepts of potential evapotranspiration and wet environmental evapotranspiration were used. The regional average groundwater levels and the specific yield were used to tune Bouchet's equation. The extrapolation of the water storage series to a secular period (1901–2002) was achieved using a synthetic annual discharge series. The water storage was deficient for most of the century, i.e. more than 60 years; nevertheless in the last 30 years, the system recovers half of the water previously lost. The singular spectral analysis showed that a significant low‐frequency signal is present in the water storage and precipitation series. The main cause of water storage variability would be given by precipitation, in spite of the vast anthropogenic changes on the basin. Anthropogenic effects would be reflected in the river discharges, where no significant signal is detected before 1970; however, an annual signal is insinuated after that year. The conclusions of this work could be different if we only looked at the 1954–1986 period. The results of that period suggest that the basin is primarily accumulating water instead of being mainly in deficit. Thus, here we demonstrated the importance of the secular analysis to illustrate the complete basin behaviour. Copyright © 2012 John Wiley & Sons, Ltd.