Intense human activities in arid areas have great impacts on groundwater hydrochemical cycling by causing groundwater salinization. The spatiotemporal distributions of groundwater hydrochemistry are crucial for studying groundwater salt migration, and also vital to understand hydrological and hydrogeochemical processes of groundwater in arid inland oasis areas. However, due to constraints posed by the paucity of observation data and intense human activities, these processes are not well known in the dried-up river oases of arid areas. Here, we examined spatiotemporal variations and evolution of groundwater hydrochemistry using data from 199 water samples collected in the Wei-Ku Oasis, a typical arid inland oasis in Tarim Basin of Central Asia. As findings, groundwater hydrochemistry showed a spatiotemporal dynamic, while its spatial distribution was complex. TDS and δ18O of river water in the upstream increased from west to east, whereas ion concentrations of shallow groundwater increased from northwest to southeast. Higher TDS was detected in spring for shallow groundwater and in summer for middle groundwater. Pronounced spatiotemporal heterogeneity demonstrated the impacts of geogenic, climatic, and anthropogenic conditions. For that, hydrochemical evolution of phreatic groundwater was primarily controlled by rock dominance and evaporation-crystallization process. Agricultural irrigation and drainage, land cover change, and groundwater extraction reshaped the spatiotemporal patterns of groundwater hydrochemistry. Groundwater overexploitation altered the leaking direction between the aquifers, causing the interaction between saltwater and freshwater and the deterioration of groundwater environment. These findings could provide an insight into groundwater salt migration under human activities, and hence be significant in groundwater quality management in arid inland oasis areas.