Groundwater plays a crucial role in sustaining water supply and irrigation in arid regions with thick vadose zones; however, the recharge mechanisms and their impact on water quality remain contentious. For flood-irrigated areas, irrigation water amount is not well known to evaluate the effect of irrigation on the recharge. In this study, we employed multiple tracers to investigate recharge mechanisms in a low-hilly region with some flood-irrigated areas, where irrigation water recharge was estimated by the chloride mass balance method combined with the tritium peak method. Deep soil samples from irrigated lands in vadose zone and groundwater from unconfined aquifers were collected to determine the contents of the water isotopes (2H, 18O, and 3H), chlorides (Cl-), and nitrates (NO3−). The findings revealed unique tritium peaks preserved in the loess vadose zone, where the recharge rate under the non-irrigated site was estimated to be only 8.6 mm yr−1, 2.4 % of the average annual precipitation. According to the estimated irrigated recharge rates, irrigation water dominates the potential diffuse recharge in vadose zone. For the aquifer recharge, we then quantified diffuse recharge (62.2 ± 4.7 %, piston flow) and focused recharge (37.8 ± 4.7 %, preferential flow) via the line-conditioned excess (lc-excess) balance method. Focused recharge occurred in low depressions, where surface runoff carrying sediments with high solutes converged in large rainfall events during wet season. Subsequently, focused mode rapidly recharges groundwater with NO3− and Cl- elevated, deteriorating water quality of phreatic aquifer. Finally, we concluded focused recharge does not dominate aquifer recharge, but significantly affects groundwater quality. These findings underscore the implications for the sustainability of agricultural water and soil resources management, emphasizing the potential impacts of soil conservation on groundwater quality in low-hilly regions.