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Climate change is affecting the discharge of headstreams from mountainous areas on the Qinghai&#8722;Tibet Plateau. To constrain future changes in discharge, it is important to understand the present-day formation mechanism and components of runoff in the basin. Here we explore the sources of runoff and spatial variations in discharge through measurements of &#948;²H and &#948;¹⁸O in the Naqu River, at the source of the Nu River, on the Qinghai&#8722;Tibet plateau, during the month of August from 2016 to 2018. We established thirteen sampling sites on the main stream and tributaries, and collected 39 samples from the river. We examined all the water samples and analyzed them for isotopes. We find a significant spatial variation trend based on one-way analysis of variance (ANOVA) (<i>p</i> &lt; 0.05) between Main stream-2 and tributaries. The local meteoric water-line (LMWL) can be described as: &#948;²H = 7.9&#948;¹⁸O + 6.29. Isotopic evaporative fractionation in water and mixing of different water sources are responsible for the spatial difference in isotopic values between Main stream-2 and tributaries. Based on isotopic hydrograph separation, the proportion of snowmelt in runoff components ranges from 15% to 47%, and the proportion of rainwater ranges from 3% to 35%. Thus, the main components of runoff in the Naqu River are snowmelt and groundwater.