Tufas, which are freshwater carbonates, are potential archives of terrestrial paleoclimate. Time series of stable isotopic compositions commonly show regular seasonal patterns controlled by temperature-dependent processes, and some perturbation intrinsic to the locality. We examined three tufa-depositing sites in southwestern Japan with similar temperate climates, to understand the origin of local characteristics in the isotopic records. Seasonal change in the oxygen isotope is principally reflected by temperature-dependent fractionation between water and calcite but was perturbed after heavy rainfalls overwhelming the stability of the δ 18 O value of the groundwater at one site. Isotopic mass balance indicates an undersaturated and relatively small aquifer at this locality. Water δ 18 O values at the other two sites were stable, reflecting a regular seasonal change in the δ 18 O value of tufa. Perturbation of the δ 13 C values in tufa is largely due to CO 2 degassing from the stream, which significantly increases the δ 13 C values of dissolved inorganic carbon (DIC). At a site with remarkably high pCO 2 in springwater and a sensitive response of flow rate to rainfall, the amount of CO 2 degassing changed distinctly with flow rate. In contrast, the other two sites having low pCO 2 springwater reflect a regular seasonal pattern of δ 13 C in DIC and tufa specimens.