The Allier River and its alluvial aquifer constitute a shallow but highly productive water resource due to their hydrodynamic properties. This hydrosystem provides almost all of the water requirements for domestic supply and irrigation. Recent dry summers (such as those in 2015, 2019, and 2022) and the lack of winter recharge have led managers to question the sustainability of this resource. We proposed the use of hydrological modelling with Gardenia with which the water balance can be determined at the watershed scale (7020 km2) and with which forecasting simulations can be performed for 2030–2070. Thus, this work was divided into (1) model calibration (2000–2020), (2) the determination of the main drivers of the water balance (2000–2020), (3) and river flow and groundwater level simulation (2030–2070). For the latter, Gardenia was used considering a “better case”, using the RCM Aladin63 in RCP2.6, and considering a “worst case”, using the RCM RegCM4-6 in RCP8.5. The calibration for 2000–2014 showed good reproducibility of river flows (NSE = 0.91) and groundwater levels (NSE = 0.85). The model showed that the major drivers in 2000–2020 were actual evapotranspiration and effective precipitation, which, respectively, represented 68% and 32% of mean annual precipitation. Water withdrawals did not significantly contribute to the water balance with the exception of those in very dry summers, such as those in 2003, 2005, 2015, and 2019. Climate appeared, therefore, as a prevalent factor of the Allier hydrosystem functioning compared to global withdrawals except for that during these dry years. Prospective simulations showed a decline in annual river flows and groundwater levels by a maximum of −15% and −0.08 m asl (“worst case”), respectively. These simulations showed that the Allier hydrosystem will be able to meet the water needs for various uses until 2070. In detail, it is likely that summer shortages will no longer be compensated by the Naussac Dam if the hydrosystem faces more than two years of drought. In this case, water-saving solutions will have to be found. This study is, thus, a good example of the application of hydrological modelling to address management issues in such a hydrosystem.