The Chingshui geothermal field, a moderate-temperature and water-dominated hydrothermal system, was the site of the first geothermal power plant in Taiwan. Many geological, geophysical and geochemical studies using more than 21 drilled wells have been performed since the 1960s. However, there are still controversies regarding the heat and fluid sources due to the tectonically complicated geological setting. To clarify the heat and fluid sources, we analyzed clumped isotopes with carbon and oxygen isotopic compositions of calcite scaling in geothermal wells and veins on outcrops and calculated the δ18O values of the source fluids. Two populations of δ18O values were calculated: −5.8 ± 0.8‰ VSMOW from scaling in the well and −1.0 ± 1.6‰ to 10.0 ± 1.3‰ VSMOW from outcropping calcite veins, indicative of meteoric and magmatic fluid sources, respectively. Meanwhile, two hydrothermal reservoirs at different depths have been identified by magnetotelluric (MT) imaging with micro-seismicity underneath this area. As a result, we propose a two-reservoir model: the shallow reservoir provides fluids from meteoric water for the scaling sampled from wells, whereas the deep reservoir provides magmatic fluids from deep marble decarbonization recorded in outcropping calcite veins.