The impacts of long-term pumping on groundwater flow patterns and groundwater chemistry are unclear in the Manas River Basin, an arid inland basin in Northwest China. In this study, hydraulic heads, hydrochemistry and environmental isotopic tracers were analyzed to reveal groundwater flow patterns, recharge sources and deduce hydrogeochemical processes in this highly exploited aquifer system. Spatial trends in the isotopic ratios delta O-18 and delta H-2 indicate that groundwater originates from glacial melting and precipitation in the mountainous area. In the piedmont plains, dissolution of calcite, gypsum and dolomite yields a groundwater type dominated by Ca-HCO3-SO4 with TDS of 300 mg/L. In this area, high H-3 concentrations demarcate local flow systems and imply modern precipitation recharge. Downgradient in the lowlands, irrigation return flow recharges shallow groundwater through local flow paths. Groundwater pumping has intensified vertical hydraulic gradients causing vertical mixing between aquifers. Generally, across the basin, regional flow systems contain groundwater with C-14 ages ranging from modern to 33,000 years, with the oldest waters found in wells with depths greater than 200 m. From high to low elevation groundwater chemistry transitions from Ca-HCO3-SO4 to Na-Cl-SO4 type as concentrations of Cl and overall TDS increase. The replacement of Ca2+ with Na+ as the dominant cation suggests reverse ion exchange and carbonate precipitation occur along the intermediate and regional flow paths. Anthropogenic activities (i.e. pumping, irrigation return flow, application of fertilizers) impact shallow groundwater chemistry (<60 m). This research reveals the impacts of natural and human-induced hydrogeochemical processes impacting groundwater chemistry in this basin with implications for similar semi-arid to arid, inter-montane basins around the world.