Typical geothermal systems in the Da Qaidam (DQ) and Gonghe–Guide Basin (GGB) on the northeastern Tibetan Plateau (NETP) discharged different BLi contents. A widely accepted metallogenic model is that the salt–lake type BLi deposits in the TP are recharged by geothermal fluids with B–Li–rich, carried by rivers and enriched in the terminal salt lakes. The B–Li–rich geothermal water is the key source of mineralization in salt lakes, however, enrichment mechanism governing differential BLi contents in DQ and GGB geothermal systems remains ambiguous. This study systematically deciphers water chemistry and isotope characteristics (δD, δ18O, δ11B, δ7Li) of river waters, geothermal waters, sinters and surrounding rocks to discuss the enrichment process of BLi elements in the DQ and GGB geothermal systems. The δD and δ18O values of geothermal systems in the DQ (δD = −79.60 ∼ −82.40 ‰, δ18O = −10.97 ∼ −11.38 ‰) and GGB (δD = −64.00 ∼ −97.10 ‰, δ18O = −8.70 ∼ −13.00 ‰) are close to the GMWL and LMWL, indicating meteoric origin. The δD and high Cl− values (300–900 mg/L) of geothermal waters in the DQ and Qiabuqia, Qunaihai, Zhacangsi along Riyueshan of the GGB imply that these geothermal waters mixed by magmatic fluid and meteoric water. The hot springs in the DQ (B = 38.35–46.29 mg/L, Li = 3.11–3.72 mg/L) and GGB (B = 0.17–8.16 mg/L, Li = 0.08–10.49 mg/L) exhibit differential BLi geochemical characteristics. B and Li contents are higher in DQ hot springs and in hot springs along Riyueshan of the GGB, respectively. Comparison of the BLi contents and δ11B–δ7Li values of geothermal waters, sinters and host rocks reveals that BLi contents of geothermal waters are controlled by B–rich HP-UHP metamorphic rocks formed by metamorphism and Li–rich granites or pegmatites formed by magmatism in the Qilian Shan, respectively. Moreover, metamorphic and magmatic processes, combining with deep circulation reactivated by the thrust or strike–slip faults, create differential enrichment of BLi elements in the geothermal systems, such as DQ and GGB on the NETP. This study highlights into understanding the differential enrichment of BLi in the geothermal system on the TP. Furthermore, the resource elemental abundance of geothermal waters can be applied as an important prospecting indicator of endogenous BLi deposits.