© 2017 Elsevier B.V. Exhumation and accompanying retrograde metamorphism alter the compositions and textures of metamorphic rocks through deformation, mineral–mineral reactions, water–rock reactions, and diffusion-controlled intra- and inter-mineral atomic mobility. Here, we demonstrate that these processes are recorded in the clumped- and single-isotope (δ13C and δ18O) compositions of marbles, which can be used to constrain retrograde metamorphic histories. We collected 27 calcite and dolomite marbles along a transect from the rim to the center of the metamorphic core-complex of Naxos (Greece), and analyzed their carbonate single- and clumped-isotope compositions. The majority of Δ47 values of whole-rock samples are consistent with exhumation- controlled cooling of the metamorphic complex. However, the data also reveal that water–rock interaction, deformation driven recrystallization and thermal shock associated with hydrothermal alteration may considerably impact the overall distribution of Δ47 values. We analyzed specific carbonate fabrics influenced by deformation and fluid–rock reaction to study how these processes register in the carbonate clumped-isotope system. Δ47 values of domains drilled from a calcite marble show a bimodal distribution. Low Δ47 values correspond to an apparent temperature of 260 °C and are common in static fabrics; high Δ47 values correspond to an apparent temperature of 200 °C and are common in dynamically recrystallized fabrics. We suggest that the low Δ47 values reflect diffusion-controlled isotopic reordering during cooling, whereas high Δ47 values reflect isotopic reordering driven by dynamic recrystallization. We further studied the mechanism by which dynamic recrystallization may alter Δ47 values by controlled heating experiments. Results show no significant difference between laboratory reactions rates in the static and dynamic fabrics, consistent with a mineral-extrinsic mechanism, in which slip along crystal planes was associated with atomic-scale isotopic reordering in the calcite lattice. An intrinsic mechanism (enhanced isotopic reordering rate in deformed minerals) is contraindicated by these experiments. We suggest that Δ47 values of dynamically recrystallized fabrics that form below the diffusion-controlled blocking-temperature for calcite constrain the temperature of deformation. We find that Δ47-based temperatures of static fabrics from Naxos marbles are ∼60–80 °C higher than commonly observed in slowly cooled metamorphic rocks, and would suggest cooling rates of ∼105°CMyr−1. A similar thermal history is inferred for dolomite marbles from the core vicinity, which preserve apparent temperatures up to 200 °C higher than a typical blocking temperature (∼300 °C). This finding could be explained by a hydrothermal event driving a brief thermal pulse and locally resetting Δ47 values. Rapid cooling of the core-complex region is consistent with a compilation of published cooling ages and a new apatite U–Th/He age, associating the thermal event with the emplacement of a granodiorite pluton at ∼12 Ma.