Accurate estimation of groundwater recharge in regions with limited water and thick unsaturated zones is challenging because of the limited water flux. This study aims to employ multiple tracers and methods to investigate the mechanism of groundwater recharge in the thick loess deposits of China. We collected soil samples under different vegetation, unconfined groundwater, and precipitation to determine the water isotopes (δ²H, δ¹⁸O, and ³H), chloride (Cl^-), nitrate (NO₃^–). Then, these tracers were employed to estimate recharge rates with methods considering the differences in shallow- and deep-rooted vegetation, as well as those in unsaturated and saturated zones. Results indicated that local precipitation predominantly recharges groundwater through matrix flow at a velocity of 14.5 cm year⁻¹ with the residence time of > 200 years. The recharge rates range from 0 to 37 mm year⁻¹, equivalent to 0–7% of annual average precipitation. However, the deep-rooted vegetation greatly reduced deep drainage compared with shallow-rooted vegetation, which will perturb the current hydraulic connectivity between unsaturated and saturated zones. The multiple tracers and methods can complement each other to enhance the understanding of groundwater recharge mechanisms. The indicated relationship between recharge form and land use suggests the urgency in developing strategies to balance the agroforestry system and water resource sustainability.