The utilization for water resource has been of great concern to human life. To assess the natural water system in Kangding County, the integrated methods of hydrochemical analysis, multivariate statistics and geochemical modelling were conducted on surface water, groundwater, and thermal water samples. Surface water and groundwater were dominated by Ca-HCO3 type, while thermal water belonged to Ca-HCO3 and Na-Cl-SO4 types. The analyzing results concluded the driving factors that affect hydrochemical components. Following the results of the combined assessments, hydrochemical process was controlled by the dissolution of carbonate and silicate minerals with slight influence from anthropogenic activity. The mixing model of groundwater and thermal water was calculated using silica-enthalpy method, yielding cold-water fraction of 0.56–0.79 and an estimated reservoir temperature of 130–199 °C, respectively. δD and δ18O isotopes suggested that surface water, groundwater and thermal springs were of meteoric origin. Thermal water should have deep circulation through the Xianshuihe fault zone, while groundwater flows through secondary fractures where it recharges with thermal water. Those analytical results were used to construct a hydrological conceptual model, providing a better understanding of the natural water system in Kangding County.