The Mesoproterozoic North American Midcontinent Rift hosts the world’s largest accumulation of native copper in Michigan’s Keweenaw Peninsula. During a regional metamorphogenic-hydrothermal event, native copper was deposited along with spatially zoned main-stage minerals in a thermal high. This was followed by deposition of late-stage minerals including minor copper sulfide. Inferences from the oxygen and carbon isotopic composition of main-stage hydrothermal fluids, as calculated from 296 new and compiled isotopic measurements on calcite, are consistent with existing models that low-sulfur saline native copper ore-forming fluids were dominantly derived by burial metamorphic processes from the very low sulfur basalt-dominated rift fill at depth below the native copper deposits. Co-variation of oxygen and carbon isotopic compositions are consistent with mixing of metamorphic-derived fluids with two additional isotopically different fluids. One of these is proposed to be evolved seawater that provided an outside source of salinity. This fluid mixed at depth and participated in the formation of a well-mixed hybrid metamorphic-dominated ore-forming fluid. Secondary Ion Mass Spectrometry in-situ isotopic analyses of calcite demonstrate a high degree of variability within samples that is attributed to variable degrees of shallow mixing of the hybrid ore-forming fluid with sulfur-poor, reduced evolved meteoric water in the zone of precipitation. The oxygen and carbon isotopic compositions of 100 new and compiled measurements on late-stage calcite are mostly isotopically different than the main-stage hydrothermal fluids. The late-stage hydrothermal fluids are interpreted as various proportions of mixing of evolved meteoric water, main-stage hybrid ore-forming fluid, and shallow, evolved seawater in the relatively shallow zone of precipitation.