Changes of groundwater flow and quality were investigated in a subtropical karst aquifer to determine the driving mechanism. Decreases in groundwater flow are more distinct in discharge zones than those in recharge and runoff zones. Long-term measurement of the represented regional groundwater outlet reveals that groundwater discharge decrease by nearly 50% during the dry season. The hydrochemistry of groundwater in the runoff and discharge zones is of poorer quality than in the recharge zone. Indications of intensive land resource exploitation and changes in land use patterns were attributed to changes in groundwater conditions since 1990, but the influence of climate change was likely from 2001, because the water temperature exhibited increasing trends at a mean rate of 0.02 °C/yr even though groundwater depth was high in the aquifer. These conclusions imply the need for further groundwater monitoring and reevaluation to understand the resilience of aquifer during urbanization and development.