An increase in temperature changes the groundwater density and viscosity, therefore, it is expected that the soil hydraulic conductivity varies with temperature. Beyond this point, thermal loading induces volumetric changes for both sand and clay and may alter soil fabric. These variations might increase or decrease the intrinsic permeability of the soil. A modified temperature-controlled triaxial permeameter cell was used in this study to elevate soil temperature from 20 °C to 80 °C. Moreover, the setup was designed to control the temperature and pressure of the permeant water injected into the specimen. The hydraulic conductivity of both Ottawa sand and Kaolin clay under different confinement stresses (69 kPa to 690 kPa) was measured. Then, intrinsic permeability was calculated considering water properties variation with temperature. The results determined that, although hydraulic conductivity increases with temperature for both Ottawa sand and Kaolin clay, the intrinsic permeability of Ottawa sand reduces by 50%, while in Kaolin clay it slightly reduces when the temperature rises from 20 °C to 80 °C. Nonetheless, analyzing volumetric changes and void ratio variations for both selected soil types show a reduction in void ratio with temperature. Reduction in the void ratio can explain the lower intrinsic permeability in Ottawa sand at the elevated temperature, however in Kaolin clay despite the higher void ratio reduction, another mechanism which is the degeneration of a part of the immobile water within the structure into the mobile water plays an important role.