The Tibetan Plateau is the “Asia Water Tower” and is pivotal for Asia and the whole world. Groundwater is essential for sustainable development in its alpine regions, yet its chemical quality increasingly limits its usability. The present research examines the hydrochemical characteristics and origins of phreatic groundwater in alpine irrigation areas. The study probes the chemical signatures, quality, and regulatory mechanisms of phreatic groundwater in a representative alpine irrigation area of the Tibetan Plateau. The findings indicate that the phreatic groundwater maintains a slightly alkaline and fresh status, with pH values ranging from 7.07 to 8.06 and Total Dissolved Solids (TDS) between 300.25 and 638.38 mg/L. The hydrochemical composition of phreatic groundwater is mainly HCO3-Ca type, with a minority of HCO3-Na·Ca types, closely mirroring the profile of river water. Nitrogen contaminants, including NO3−, NO2−, and NH4+, exhibit considerable concentration fluctuations within the phreatic aquifer. Approximately 9.09% of the sampled groundwaters exceed the NO2− threshold of 0.02 mg/L, and 28.57% surpass the NH4+ limit of 0.2 mg/L for potable water standards. All sampled groundwaters are below the permissible limit of NO3− (50 mg/L). Phreatic groundwater exhibits relatively good potability, as assessed by the entropy-weighted water quality index (EWQI), with 95.24% of groundwaters having an EWQI value below 100. However, the potential health risks associated with elevated NO3− levels, rather than NO2− and NH4+, merit attention when such water is consumed by minors at certain sporadic sampling locations. Phreatic groundwater does not present sodium hazards or soil permeability damage, yet salinity hazards require attention. The hydrochemical makeup of phreatic groundwater is primarily dictated by rock–water interactions, such as silicate weathering and cation exchange reactions, with occasional influences from the dissolution of evaporites and carbonates, as well as reverse cation-exchange processes. While agricultural activities have not caused a notable rise in salinity, they are the main contributors to nitrogen pollution in the study area’s phreatic groundwater. Agricultural-derived nitrogen pollutants require vigilant monitoring to avert extensive deterioration of groundwater quality and to ensure the sustainable management of groundwater resources in alpine areas.