<p>Transient processes play a major role in geophysical applications. In this paper, we quantify the significant influence arising from transient processes for conductive heat transfer problems for sedimentary basin systems. We demonstrate how the thermal properties are affected by changing the system from a stationary to a non-stationary system and what impact transient boundary conditions (derived from paleoclimate information) have. Furthermore, we emphasize the importance of time-stepping approaches and the simulation duration since both factors influence the sensitivities of the thermal properties. We employ global sensitivity analyses to quantify not only the impact arising from the thermal properties but also their parameter correlations. Furthermore, we show how the results of the sensitivity analysis can be used to gain further insights into the complex Central European Basin System. This computationally very demanding workflow becomes feasible through the construction of high precision surrogate models using the reduced basis method.</p>