Sources of volcanic and non-volcanic thermal sources have been studied in East Malaysia to differentiate their geothermal reservoir temperatures and first-ever reports on its geochemical processes that affect the evolution of the constituents of thermal groundwater subsurface circulation. The study of geothermal potentials includes indices of geochemistry, geothermometry, and mineral saturation. The surface temperatures of thermal springs range from 27 to 56 °C, and the pH values range from 5.6 to 9.0. The geochemical characteristic distinguishes non-volcanic thermal sources as K-Na-HCO3, while volcanic thermal sources present the Cl-HCO3-SO4-Na type. The quartz geothermometer showed that the reservoir temperatures of non-volcanic hot springs range between 61 and 135 °C. In comparison, the volcanic thermal sources range from 55 to 185 °C requiring 257 to 565 kJ/kg and energy from 231 to 786 respectively to heat water. Subsequently, it is defined as intermediate to slightly high enthalpy for most thermal springs, especially volcanic springs. The mixing of hot water with sources close to the surface can be seen by the disagreement between the silica and cation geothermometers and the disequilibrium with their associated host rocks as indicated from the plot of studied hot springs in the Na-K-Mg ternary diagram and saturation indices calculations. Radiogenic granitic host rock represents the main heat source for non-volcanic hot springs govern by meteoric water generated in deep-seated fault systems. Meanwhile, in volcanic areas with high secondary permeability caused by faults, fractures and fractures, meteorological waters can descend to a considerable depth and heat up. In a favourable situation, thermal waters return to the surface by faults and fracture zones. © 2021 Elsevier Ltd