Many geothermal reservoirs in Chongqing in southwestern China are located in carbonate rock aquifers and exploited through drilling. Water samples from 36 geothermal wells have been collected in the main urban area of Chongqing. Chemical types of the thermal water samples are Ca·Mg-SO4 and Ca-SO4. High contents of Ca2+ and SO42− in the thermal water samples are derived from the dissolution of evaporates. Furthermore, the HCO3− concentration is constrained by the common ion effect. Drilling depth has no effect on the physical and chemical characteristics according to the results of a t-test. The geothermal reservoir’s temperature can be estimated to be 64.8–93.4°C (average 82°C) using quartz and improved SiO2 geothermometers. Values of δD and δ18O for the thermal water samples indicate that the thermal water resources originate from local precipitation with a recharge elevation between 838 and 1130m and an annual air temperature between 10.4 and 13.9°C. A conceptual model of regional scale groundwater flow for the thermal water is proposed. The thermal water mainly originates from the meteoric water recharged in the elevated areas of northeastern Tongluoshan and Huayingshan by means of percolation through exposed carbonate before becoming groundwater. The groundwater is heated at depth and moves southwest along the fault and the anticlinal core in a gravity-driven regime. The thermal water is exposed in the form of artesian hot springs in river cutting and low-elevation areas or in wells.