A variation of temperature produces a change in the microstructure of the rock due to the mineral thermal expansion and its residual strain. Depending on the temperature cycle and texture, microstresses may lead to the development of preexistent cracks or the creation of a new and irreversible cracking. The effect of temperature on reservoir rocks is an important topic since it conditions the permeability and the fluid flow. Two main questions arise from this: the first is if an irreversible cracking threshold is attained in the reservoir rocks at low temperature geothermal systems (around 100 °C); the second one is about the influence of thermal fatigue by the repetition of heating–cooling cycles on the different rock types. To answer these questions, four reservoir rocks (chalk, sandstone, fresh granite, and weathered granite) were submitted to two different thermal regimes. The first test was conceived to detect the irreversible cracking threshold, and for that, the rocks were submitted to progressive heating (90°, 100°, 110°, 120°, and 130 °C). The second test consisted of doing cycles of fast heating of the samples up to 200 °C. The microstructure variation was assessed by means of a scanning electron microscope, mercury porosimetry, and capillary water uptake combined with passive infrared thermography. Infrared thermography is an emerging tool in the field of rock study, used to detect water masses or determine thermal properties. The water transfer during the capillary tests of the rocks, before and after the tests, was monitored with this technique. In addition, the cooling rate index, a non-destructive parameter to detect cracking development, was calculated. The results made it possible to differentiate the behaviours in relation to the rock type, with a chalk and a weathered granite less susceptible to thermal stresses than a fresh granite and sandstone. In addition, infrared thermography resulted in being a very useful indirect technique to detect the changes on the surface, although they do not always correlate to the bulk microstructural changes.