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Hidden geothermal systems represent resources which are characterized by the absence of surface expressions of hydrothermal activity. Economic geothermal development is favored in reservoirs which are controlled by convective heat transfer. Basin modeling provides information on the pressure and thermal regime and can identify areas where conductive or convective transfer processes are dominant. We present a basin modeling workflow for hidden geothermal systems from regional screening towards the prediction of localized, thermally anomalous patterns. This workflow has been applied to the thermally complex Upper Rhine Graben (France, Germany). It integrates a crustal modeling approach to predict the regional rift-related thermal regime, diagenetic reactions to evaluate the risk of cementation on porosity reduction, and systematic calibration methods to identify areas where heat transferred by convection might be significant. In addition, we integrated the Rayleigh number which is a measure for free convection in systems described by fluid mechanics. This number helps to localize areas where convection cells are likely to affect heat transfer, i.e., where a purely conductive heat flow is not sufficient to describe the total heat transport in the porous medium.