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The Molasse Basin in Southern Germany is part of the North Alpine Foreland Basin and hosts the largest accumulation of deep geothermal production fields in Central Europe. Despite the vast development of geothermal energy utilization projects especially in the Munich metropolitan region, the evolution of and control factors on the natural geothermal field, more specifically the time-varying recharge and discharge governing groundwater and heat flow, are still debated. Within the Upper Jurassic (Malm) carbonate aquifer as the main geothermal reservoir in the Molasse Basin, temperature anomalies such as the Wasserburg Trough anomaly to the east of Munich and their underlying fluid and heat transport processes are yet poorly understood. We delineate the two end members of thermal–hydraulic regimes in the Molasse Basin by calculating two contrasting permeability scenarios of the heterogeneously karstified Malm carbonate aquifer along a model section through the Wasserburg Trough anomaly by means of two-dimensional numerical thermal-hydraulic modelling. We test the sensitivity of the thermal-hydraulic regime with regard to paleoclimate by computing the two Malm permeability scenarios both with a constant surface temperature of 9 °C and with the impact of paleo-temperature changes during the last 130 ka including the Würm Glaciation. Accordingly, we consider the hydraulic and thermal effects of periglacial conditions like permafrost formation and the impact of the numerous glacial advances onto the Molasse Basin. Thermal-hydraulic modelling reveals the effect of recurrent glacial periods on the subsurface targets of geothermal interest, which is minor compared to the effect of permeability-related, continuous gravity-driven groundwater flow as a major heat transport mechanism. [ABSTRACT FROM AUTHOR]