The stable-isotope composition of a tufa collected on subtropical Miyako Island, southern Japan, records climatic and hydrologic changes over a 15-year period (1989–2003). A total of 450 subsamples taken at increments of 0.2 mm define the high-resolution isotopic profile of a 9-cm-long sample. The oxygen isotope values clearly exhibit cyclical changes that generally correlate with the annual lamination pattern of the tufa. The observed stability of water δ18O values confirms that the seasonal records of water temperature are reflected in the cyclic change of tufa δ18O values. The oxygen isotope profile also exhibits a long-term decreasing trend that is equivalent to a 2.5°C temperature increase over the 15-year period. The range of the long-term change in δ18O values is at least partly compensated for by a warming trend of 0.95°C seen in metrological data for Miyako Island. However, the carbon isotope profile does not vary cyclically, and the values are clearly higher than for previously reported tufas from the temperate Japanese mainland. Vegetation on Miyako Island, which is dominated by C4-type sugar cane, is largely responsible for the high δ13C values of the tufa. The high-resolution isotopic profile provides data on the annual deposition rate, which clearly increased from 1996 to 1998, when the groundwater table was raised by the construction of two underground dams near the tufa locality. Increased water flow from the spring activated calcite precipitation and increased the depositional rate in the upper part of the core up to > 1 cm/year. This rate is much larger than those recorded for tufas from temperate settings in Japan.