Since traditional graphical methods are weak to provide a reliable result for assessing the hydrothermal circulation depth and mixing processes, principal component analysis (PCA) and inverse geochemical modeling are used to evaluate the relation between the chemical and physical parameters affecting the spatiotemporal composition of Semnan thermal springs. These waters belong to the Na-Cl water type, with the total dissolved solids of about 9847-mg/L and mean temperature of 31.5 °C. PCA extracted three components that explain 87.89% of the sample variances from a matrix of 35 monthly samples, taken from five thermal springs and analyzed for ten variables. Based on the results of the PCA, the water-rock interactions including evaporate dissolution, cation exchange, and dedolomitization control the chemical composition of thermal waters, and dilution by aquifer recharge creates the seasonal variation in water quality. Geochemical mass-balance modeling simulates the microbial SO4 reduction and silicate weathering and allows quantification of the evolution of the hydrothermal system. Based on the isotopic data, the meteoric water is the major origin of thermal waters without oxygen-18 shift. In addition, Chenaran anticline is the most probable catchment area of thermal springs based on the water balance calculation and geological setting. These results are quite convenient with the previous hydrological conceptual model obtained from the geochemical data. The present study highlights the importance of applying both PCA and inverse modeling simultaneously with conventional methods for assessing the origin of thermal water and deep understanding of predominant processes controlling the hydrogeochemical evolution in a carbonate aquifer includes low enthalpy thermal waters. This methodology has the potential for application in other regions with similar condition.