The Nalenggele River Catchment (NRC) is the largest river sourced from the northern slope of the Eastern Kunlun Mountains (EKM). The NRC terminates in the Qaidam Basin and feeds tail salt lakes. The river–groundwater system (freshwater) and the terminal salt lakes display high concentrations of B and Li, ranking the Qaidam Basin as a world-class mineral system. However, the source, pathway, and enrichment mechanism of these elements remain unclear. In this study, the B and Li isotopes from rivers and groundwater from mountain to basin were used to trace their origin and evolution processes. B and Li are found in high concentrations even in river and groundwater with low total dissolved solids (TDS), with average concentrations tens to hundreds times higher than those of natural freshwater systems. The observed B and Li isotopic footprints are significantly depleted in heavy isotopes in the NRC if compared to other geological systems dominated by natural weathering processes. Following the confluence of one of the main tributaries of the Hongshui River (HSR) sourced from the EKM, the B and Li concentrations increase sharply, while the δ11B and δ7Li values gradually decrease. This study indicates that the mechanism accounting for the B and Li endowment of the river–groundwater–salt lake system is mainly related to the Li-B fertility of the sources (deep fluids and country rocks), favorable tectonic conduits for water circulation, and high evaporation rates. Specifically, the deep fluids upwelling is responsible for the sourcing of B and Li. These fluids are then discharged to the river and groundwater through geothermal springs developing along deep faults or within volcanic craters. In this frame, the river and groundwaters act as carriers, and input B and Li into the lake basin. Ultimately, B and Li undergo an evaporation-mediated fractionation ending with the formation of brines and eventually accounting for the formation of the world-class Li–B salt lake deposits.