Groundwater is a critical lifeline for ecosystems and human settlements in arid and semi-arid regions, yet it is increasingly vulnerable to the dual pressures of extreme climatic conditions and intensifying anthropogenic activities. This study investigated 24 groundwater and 4 river water samples to discuss the hydrogeochemical evolution and water quality suitability in the Tianjun Basin, a typical high-altitude arid basin on the northeastern Tibetan Plateau. The results indicate that groundwater is mildly alkaline (pH: 7.65–8.35) and predominantly fresh (TDS: 233.77–1061.42 mg/L). Hydrochemical facies evolve from HCO₃-Ca type in upstream areas to Mixed HCO₃-Na·Ca and Cl-Na types. Hydrochemical analysis suggests that silicate weathering and carbonate dissolution are the dominant natural processes, while cation exchange further modifies the ionic composition. Notably, anthropogenic nitrogen (NO₃⁻ and NH₄⁺) contamination, primarily from domestic sewage in the Tianjun Basin, has significantly impacted groundwater quality. Health risk assessment shows that infants are the most vulnerable group, with 16.67% of samples posing a non-carcinogenic risk via the oral pathway. Regarding irrigation suitability, while sodium hazards are generally low, a significant salinity hazard is identified due to elevated electrical conductivity in the arid environment. This poses a substantial risk of secondary soil salinization, necessitating strict salt management strategies to preserve long-term land productivity. These findings provide critical insights for the sustainable management of fragile groundwater resources in extreme arid environments.