The geochemical and ultrastructural properties of thermally altered skeletal carbonate are expected to be compromised to varying degrees by disequilibrium processes between solids and the ambient aqueous fluids. When assessing the alteration history of carbonates, it is important to apply models that quantitatively describe these diagenetic processes on multiple geochemical systems, such that they can be identified in natural samples. Carbonate clumped isotope analysis provides a unique tool for validating such models and can be combined with other geochemical tools/proxies to more comprehensively describe the processes and products. Here, we have analyzed bivalve shells that have undergone hydrothermal alteration (experimental diagenesis) in high water/rock ratio experiments at 130 and 160{degree sign}C, demonstrating that non-linear changes in ∆47 and ∆48 values can be attributed to heterogeneous replacement of precursor carbonates. Importantly, this model predicts decoupled ∆47 and ∆48 values, despite all reactions occurring at clumped isotope equilibrium with respect to the experimental temperature. We demonstrate that the rapid, thermally induced re-equilibration occurs in a “closed system” with minimal exchange with the ambient fluid, similar to the results of heating experiments conducted without an extraneous fluid. Later stages of alteration occur in an “open system” wherein internal fluid is exchanged with the external fluid at a similar rate to recrystallization and neomorphism. In these experiments, some oxygen from the original inorganic-organic composite-biomineral is inherited, indicating restrictions on the availability of fluid oxygen. Our experiments and models validate a novel application for dual-clumped isotopes for reconstructing hydrothermal temperatures and fluid δ18O compositions.