Paleoenvironmental reconstructions based on the clumped isotopes (Δ47) and traditional isotope (δ13C or δ18O) techniques are often problematic for carbonates that have undergone diagenetic alteration. One of the most common types of diagenesis is the transition between polymorphs, such as the replacement of aragonite by calcite. The isotope fractionation during such transitions in aqueous solutions remains unclear. We conducted a series of aragonite-to-calcite transition experiments in aqueous solutions of varying salinity and experiment durations at 25 °C and 90 °C to examine the variations of δ13C, δ18O, and Δ47 values for carbonates at varying degrees of the transition. The results confirm the retarding effect of Mg2+ and the catalytic effect of Na+ and Ca2+ on the transition, which are consistent with previous findings. Compared with the results from the transitions at 25 °C, the 90 °C experiments show a greater transition to calcite and a more depleted oxygen isotope composition. However, both clumped and carbon isotope values show no significant variation in the various experiments, suggesting that they are unaffected by mineralogical transition. Based on published equilibrium calibrations for δ18O and Δ47, the results demonstrate that kinetic effects in isotope systems are controlled primarily by the rate of polymorph transition, but there is a significant kinetic difference between the clumped isotope bond (13C 18O) reordering and the 18O exchange within the dissolved inorganic carbon pool. This kinetic difference results in partial equilibration in δ18O with no significant reordering in Δ47 toward their equilibriums, which can be accounted for by the difference of equilibration rates between the oxygen isotopes bound to 12C and those bound to 13C. This study provides a clear observation of the response of isotope systems to carbonate polymorph transitions and sheds light on their reliability as paleoenvironmental proxies.