The use of clumped isotopes (Δ47) as a geothermometer in carbonates has become widespread in geosciences because carbonates are ubiquitous in the environment and this technique also constrains the precipitating fluid δ18O composition. However, in some contexts, Δ47 values cannot be used as a geothermometer. Instead, they provide insights into processes affecting the isotopic composition of CO2 and dissolved inorganic carbon (DIC) prior to and during precipitation, as observed in speleothems, corals, and cold seep-associated authigenic carbonates. Among all these precipitates, authigenic carbonates associated with cold seeps stand out, as the measurement of their clumped isotopic abundances has revealed an unprecedented range of isotopic ordering, and several explanations were put forward to explain the various signals observed. To get a firmer understanding of the cause of natural variability in modern cold seeps, here we report δ13C, δ18O and Δ47 results performed on carbonates from two deep-sea cold seeps offshore Nova Scotia, Canada, i.e., >2300 m water depth and within the gas hydrate stability zone. We report a broad Δ47 range (i.e., 0.502–0.663 ‰ I-CDES) that differs from values expected at isotopic equilibrium at seafloor temperatures (i.e., 0.671–0.672 ‰ I-CDES). Using micro computed X-ray tomography, micro-X-ray fluorescence, and micro sampling, we demonstrate that methane-derived authigenic carbonates at these deep-water sites are closely associated with colocalized methane-hydrate dissolution. The isotopic composition of these authigenic carbonates are influenced by the complex mixing of different dissolved inorganic carbon (DIC) pools at various stages of isotopic re-equilibration, resulting in fine-scale isotopic variability. We propose several mixing models and stages of DIC re-equilibration to explain this isotopic variability and apply them to evaluate the contributions of the proposed sources of DIC. The isotopic domains resulting from this exercise encompass the entire range of dual isotopic values (δ18O and Δ47) ever observed in cold seeps and suggests that the isotopic diversity observed in these environments may be broader than that observed to date.