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Abstract Clumped isotope paleothermometry using pedogenic carbonates is a powerful tool for investigating past climate changes. However, location‐specific seasonal patterns of precipitation and soil moisture cause systematic biases in the temperatures they record, hampering comparison of data across large areas or differing climate states. To account for biases, more systematic studies of carbonate forming processes are needed. We measured modern soil temperatures within the San Luis Valley of the Rocky Mountains and compared them to paleotemperatures determined using clumped isotopes. For Holocene‐age samples, clumped isotope results indicate carbonate accumulated at a range of temperatures with site averages similar to the annual mean. Paleotemperatures for late Pleistocene‐age samples (ranging 19–72 ka in age) yielded site averages only 2°C lower, despite evidence that annual temperatures during glacial periods were 5–9°C colder than modern. We use a 1D numerical model of soil physics to support the idea that differences in hydrologic conditions in interglacial versus glacial periods promote differences in the seasonal distribution of soil carbonate accumulation. Model simulations of modern (Holocene) conditions suggest that soil drying under low soil pCO2 favors year‐round carbonate accumulation in this region but peaking during post‐monsoon soil drying. During a “glacial” simulation with lowered temperatures and added snowpack, more carbonate accumulation shifted to the summer season. These experiments show that changing hydrologic regimes could change the seasonality of carbonate accumulation, which in this study blunts the use of clumped isotopes to quantify glacial‐interglacial temperature changes. This highlights the importance of understanding seasonal biases of climate proxies for accurate paleoenvironmental reconstruction.