Carbonate-brucite chimneys are a characteristic of low- to moderate-temperature, ultramafic-hosted alkaline hydrothermal systems, such as the Lost City hydrothermal field located on the Atlantis Massif at 30°N near the Mid-Atlantic Ridge. These chimneys form as a result of mixing between warm, serpentinization-derived vent fluids and cold seawater. Previous work has documented the evolution in mineralogy and geochemistry associated with the aging of the chimneys as hydrothermal activity wanes. However, little is known about spatial heterogeneities within and among actively venting chimneys. New mineralogical and geochemical data (87Sr/86Sr and stable C, O, and clumped isotope) indicate that brucite and calcite precipitate at elevated temperatures in vent fluid-dominated domains in the interior of chimneys. Exterior zones dominated by seawater are brucite-poor and aragonite is the main carbonate mineral. Carbonates form mostly out of oxygen and clumped isotope equilibrium due to rapid precipitation upon vent fluid-seawater mixing. In contrast, the carbonates precipitate close to carbon isotope equilibrium, with dissolved inorganic carbon in seawater as the dominant carbon source, and have δ13C values within the range of marine carbonates. Our data suggest that calcite is a primary mineral in the active hydrothermal chimneys and does not exclusively form as a replacement of aragonite during later alteration with seawater. Elevated formation temperatures and lower 87Sr/86Sr relative to aragonite in the same sample suggest that calcite may be the first carbonate mineral to precipitate.