Scapolite occurs as the major halogen-bearing phase at all paragenetic stages of skarn formation and mineralization in the Jinshandian iron skarn deposit, Eastern China. Here we integrate geochemical characteristics of scapolite with in situ B and Sr isotopes of associated tourmaline and fluorapatite, respectively, to trace the sources and evolution of the fluids responsible for mineralization in this deposit. Pre-ore stage I scapolite has molar Cl/Br ratios ranging from ~ 920 to 2200, which, together with the boron isotope composition of pre-ore stage I tourmaline, are consistent with formation from magmatic fluids from the Jinshandian intrusion. In contrast, scapolite in syn- and post-ore stages (II and III) has significantly higher Cl/Br ratios (2900–6200) that are outside the range of magmatic fluids but are consistent with involvement of fluids derived from the halite-bearing evaporite horizons that lie within regionally extensive sedimentary country rocks. The influx of sedimentary-derived fluids is also consistent with 87Sr/86Sr of syn-ore stages II fluorapatite (0.7098–0.7109), which are significantly higher than those of the skarn-related quartz diorite intrusions (0.7058–0.7061) but approach the isotopic compositions of the Middle Triassic evaporites and other continental sedimentary country rocks. These data indicate that evaporite-sourced fluids were involved in iron ore formation at the Jinshandian deposit and may be important for the formations of other iron ore deposits. Our findings also show that scapolite halogen geochemistry in combination with other fluid tracers, such as B and Sr isotopes, can be extremely useful for identifying the origins and evolution of fluids in magmatic-hydrothermal systems.