We present a high-resolution in situ study of oxygen and boron isotopes measured in tourmaline from the world-class San Rafael Sn (–Cu) deposit (Central Andean tin belt, Peru) aiming to trace major fluid processes at the magmatic-hydrothermal transition leading to the precipitation of cassiterite. Our results show that late-magmatic and pre-ore hydrothermal tourmaline has similar values of δ18O (from 10.6 to 14.1) and δ11B (from −11.5 to −6.9). The observed δ18O and δ11B variations are dominantly driven by Rayleigh fractionation, reflecting tourmaline crystallization in a continuously evolving magmatic-hydrothermal system. In contrast, syn-ore hydrothermal tourmaline intergrown with cassiterite has lower δ18O values (from 4.9 to 10.2) and in part higher δ11B values (from −9.9 to −5.4) than late-magmatic and pre-ore hydrothermal tourmaline, indicating important contribution of meteoric groundwater to the hydrothermal system during ore deposition. Quantitative geochemical modeling demonstrates that the δ18O-δ11B composition of syn-ore tourmaline records variable degrees of mixing of a hot Sn-rich magmatic brine with meteoric waters that partially exchanged with the host rocks. These results provide thus direct in situ isotopic evidence of fluid mixing as a major mechanism triggering cassiterite deposition. Further, this work shows that combined in situ δ18O and δ11B analyses of tourmaline is a powerful approach for understanding fluid processes in dynamic magmatic-hydrothermal environments.