Background: The thermal regime of the Upper Rhine Graben (URG) is characterized by a series of anomalies near Soultz-sous-Forêts (France), Rittershoffen (France), and Landau (Germany). These temperature anomalies are associated with groundwater circulation in fractures and faults distributed in the Cenozoic and Mesozoic sedimentary cover associated with and connected to fractures originating deep within the Paleozoic basement. The present study helps to understand the convective cell structure in order to optimize geothermal borehole trajectories. Methods: The work concentrated on a detailed interpretation of the geophysical and geological logs from Soultz geothermal wells mainly from the topographic surface to the Triassic formations, at between 800-and 1,400-m depth above the deep granitic basement. Results: The analysis of drilling mud logging data and geophysical well logging data from the deep Soultz geothermal wells (GPK-2, GPK-3, GPK-4) reveals the occurrence of nine fracture zones situated at depths greater than 900 m in the limestones of the Muschelkalk (Middle Trias) and the sandstones of the Buntsandstein (Lower Trias). Based on indications of total or partial mud losses, these fracture zones have been classified as permeable or impermeable. Conclusions: Permeable fractures between circa 900-m depth and 1,400-m depth are connected to a large-scale fault and control the top of the convective cells. There is no indication of permeability in the formations above the Keuper layer, and the uppermost part of the sedimentary cover acts as a cap rock, insulating the convective regime in the Triassic sediments and the granitic basement.