In the context of climate change, it is important to understand possible future projections and historical trends of groundwater recharge, flow, and discharge to surface reservoirs. Knowledge of a vast range of possible conditions is required to fully appreciate the variability of the hydrologic cycle and hence the long-term vulnerability of groundwater-dependent habitats. This research investigates historical trends for a groundwater-surface water interacting system that supports a fragile ecosystem in southern Quebec. A transient model was developed using MODFLOW to simulate site-wide groundwater flow for the study area. The model was used to simulate past hydrogeological conditions (1900-2010) using a new data set of available precipitation (rain and snowmelt) and temperature. This data set was used to simulate the overall groundwater budget and to determine groundwater discharge (river baseflow and spring flow) in the study area. This allows for the quantification of century-long trends in flow data, as well as the extreme maximum and minimum flows over 110 years. Recharge was variable, ranging from 41 to 197 mm/year over the study period. Lower recharge rates from 1950 to 1965 induced marked effects on spring flow. Although the trend is not statistically significant, there appears to be, for the second half of the study period (1966-2010), a tendency towards a reversal to an increase for recharge, hydraulic heads, spring flow and baseflows. A longer time series would be necessary to confirm this tendency. The simulated historical trends are compared with flow projections for future scenarios (2041-2070). The confirmation that the natural system has been subjected to a wide range of climatic conditions over the last century helps to inform about its resilience. This study highlights the utility of groundwater flow modeling using historical climate data sets to gain a better understanding of long-term trends for climate change-related hydrogeological and ecohydrological studies.