Nitrates from different sources are commonly regarded as chemically identical once they enter groundwater. However, their associated risks to human health can vary, particularly in arid and semi-arid irrigated areas (ASAIAs) that rely heavily on groundwater. To elucidate the vertical mechanisms governing nitrate transformation and transport, and to clarify how groundwater depth influences drinking water safety, this study focused on the Ningxia region of China. Between 2022 and 2023, a total of 246 groundwater samples were collected from depths ranging from 0 to 120 m. Nitrogen and oxygen isotopes of nitrate were integrated with hydrogen and oxygen isotopes of water using isotopic kinetic fractionation analysis. Results show a distinct vertical pattern of nitrate "input-transformation-retention", mirrored by a corresponding "recharge-mixing-sequestration" pattern in groundwater flow. Notably, between depths of 41 and 60 m, denitrification and ammonium adsorption form a buffering interface that mitigates nitrate pollution. Extremely negative delta D values indicate long residence times and regional water mixing, facilitating the co-migration of nitrate with 18O-enriched evaporated water. As depth increases, drinking water safety improves markedly. Groundwater below 90 m exhibits nitrate-related health risks similar to those of surface water, with the primary contamination sources being manure and sewage infiltrated via Yellow River water irrigation. Manure-and sewage-derived nitrate undergoes more transformation, whereas fertilizer-derived nitrate is more accumulated. This study elucidates the vertical migration and transformation processes of multi-source nitrate in groundwater and provides a scientific foundation for safeguarding drinking water safety.