This study is geared towards evaluating the hydrological information that can be extracted from spring water temperature variations in shallow and thin aquifers of headwater catchments. A series of temperature variations (from 2013 to 2017) in four spring water sources at the Strengbach Critical Zone Observatory (CZO) was analyzed and interpreted by relying upon a coupled two-dimensional unsaturated–saturated flow and heat transfer model specifically designed for the study. Temperature variations of spring waters at the Strengbach catchment obey a seasonal non-phased and attenuated cyclicity compared with temperature inputs from the air or very shallow waters in soils. Simulation results show that, within the shallow subsurface horizons, heat transfer is mainly controlled by thermal conduction and not by fluid flow. The results also emphasize that the depth and temperature value of the thermal invariance zone are key parameters to surface temperature attenuation patterns in the first meters beneath the surface. The average maximum porosity (or saturated water content) is another important parameter impacting heat transfers in the shallow subsurface. Stronger attenuations and delays of the thermal signal occur as the porosity increases. These different results indicate that temperature variations in the spring waters, especially the attenuation and phase shift of the signals compared with incoming air-surface water temperatures, do not bring information on hydrological transfers. In very shallow systems, characteristics, such as flow velocities and water residence times, cannot be inferred from temperature variations. Nevertheless, this study suggests that spring water temperature variations could become a way of identifying the usually poorly known saturated water content and its spatial variability at the catchment scale.