Groundwater recharge supports sustainable development for drinking water and irrigated agriculture in vast areas worldwide. Human activities and climate change (e.g., uneven precipitation) have significantly impacted groundwater dynamics. A long term monitoring and sampling campaign was conducted for the major water bodies to investigate the evolution of groundwater and its capacity to support sustainable development in a subtropical agroforestry catchment in the middle of the Sichuan Basin with horizontal sedimentary bedrock (red beds), where seasonal droughts are notable. Major hydrochemical indicators, including δD and δ18O were measured to trace the water movement. The results showed that the chemical type of shallow groundwater was Ca•Mg-HCO3 or Ca-HCO3, which was mainly controlled by the weathering and hydrolysis of rocks. The interaction processes in the rainy season were stronger than those in the dry season. The isotopic signature in rainwater showed distinct seasonal pattern was strengthened by the local basin climate. The isotopic signals of groundwater responding to rainfall showed that recharge cycles of shallow groundwater in the rainy season lasted approximately 45–75 days. The optimized estimation based on mixing model and chloride ion balance (CMB) showed that the rainfall recharge ratio to shallow groundwater averaged about 27.83% (4.3%–58.0%) at event scale and the annual rainfall recharge ratios averaged about 19.36% (12.2%–45.7%). Groundwater in this region was renewed rapidly, as its groundwater storage capacity could be low with horizontal sedimentary bedrock. By revealing the water chemistry dynamics of shallow groundwater in the study area, this work preliminarily identified the groundwater recharge sources and estimated the recharge ratios by rainfall in a typical hilly area with red beds, thus providing a scientific basis for further regional assessment of groundwater resources.