Groundwater resources are vital for meeting the world's freshwater needs, providing the primary source of drinking water for nearly half the global population, and are particularly important for agriculture and industry in dry regions. The Paine Basin, situated south of Santiago, Chile, has been heavily affected by an extended mega-drought, influencing water availability for various uses. Yet, comprehensive hydrogeological studies to understand the aquifer system and establish a baseline for future actions in the basin to better manage water resources have been lacking. Therefore, this study investigates the aquifer's conditions in 1970, considered closest to its undisturbed state. It uses water table and chemical data to discern groundwater flow directions and the relationship between the river and the aquifer. Subsequent temporal analyses using Mann-Kendall tests and Theil-Sen slope estimation on DGA well-level data aim to statistically verify the significance of water level declines. The findings confirm an east-to-west groundwater flow, corroborated by chemical signatures linking the Paine waters to the Maipo River, suggesting river recharge from the aquifer during that era. However, recent trends indicate a significant drop in water levels since the mega-drought began in 2010, not aligning with the increase in groundwater extractions starting in 2005. The above highlights that additional water sources, such as river infiltration or irrigation return flow, need to be considered to explain water level variability, which highlights the hydrology of the basin. Finally, trend analysis over the last 30 years indicates that hydrodynamic conditions have changed since the initial conditions were considered in 1970.