Human activities and climate change input more reactive nitrogen into alpine lakes. Alpine saline lakes are usually located in endorheic watersheds at high-altitude areas, with no other drainage methods than evaporation, and are prone to accumulate nutrients. Meanwhile, alpine saline lakes are usually oligotrophic and sensitive to reactive nitrogen inputs, and even modest reactive nitrogen inputs may have significant effects on them, such as eutrophication. Nitrate is the main form of reactive nitrogen in lakes; therefore, clarifying the sources and transformations of nitrate in alpine saline lakes is important to prevent or mitigate eutrophication in alpine saline lakes. In this study, the sources and transformations of nitrate in Qixiangcuo Lake and its inflow rivers in the northern Tibetan Plateau were identified using dual nitrate isotopes and hydrochemistry. The results show that (1) the ranges of NO3− concentrations, δ15N − NO3−, and δ18O − NO3− values were 3.6 ~ 26.1 μg/L, − 10.5 to + 6.0‰, and − 10.4 to + 9.2‰ in Qixiangcuo Lake and 194.4 ~ 728.1 μg/L, + 5.8 ~ + 8.8‰, and − 1.9 to + 2.4‰ in its inflow rivers, respectively. The NO3− concentrations and δ15N − NO3− values were significantly lower in Qixiangcuo Lake than in its inflow rivers (P < 0.05). (2) The main sources of nitrate in both surface water and bottom water of Qixiangcuo Lake were ammonium in atmospheric deposition (mean probability estimate (MPE) 41.0% and 32.2%, respectively) and livestock manure (MPE 28.9% and 21.7%, respectively). The main sources of nitrate in the inflow rivers of Qixiangcuo Lake were domestic sewage (MPE 35.7%) and livestock manure (MPE 29.6%). (3) The main nitrogen transformation process in Qixiangcuo Lake was nitrification. The conservative mixing of multiple sources controlled the nitrate concentration and isotopic composition of Qixiangcuo Lake. Improvement in grazing area planning and the installation of sewage treatment facilities are effective measures to prevent eutrophication in Qixiangcuo Lake and its inflow rivers.