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Shallow subsurface thermal regimes in urban areas are increasingly impacted by anthropogenic activities, which include infrastructure development like underground traffic lines as well as industrial and residential subsurface buildings. In combination with the progressive use of shallow geothermal energy systems, this results in the so-called subsurface urban heat island effect. This article emphasizes the importance of considering the thermal impact of subsurface structures, which commonly is underestimated due to missing information and of reliable subsurface temperature data. Based on synthetic heat-transport models different settings of the urban environment were investigated, including: (1) hydraulic gradients and conductivities, which result in different groundwater flow velocities; (2) aquifer properties like groundwater thickness to aquitard and depth to water table; and (3) constructional features, such as building depths and thermal properties of building structures. Our results demonstrate that with rising groundwater flow velocities, the heat-load from building structures increase, whereas down-gradient groundwater temperatures decrease. Thermal impacts on subsurface resources therefore have to be related to the permeability of aquifers and hydraulic boundary conditions. In regard to the urban settings of Basel, Switzerland, flow velocities of around 1 m d− 1 delineate a marker where either down-gradient temperature deviations or heat-loads into the subsurface are more relevant. Furthermore, no direct thermal influence on groundwater resources should be expected for aquifers with groundwater thicknesses larger 10 m and when the distance of the building structure to the groundwater table is higher than around 10 m. We demonstrate that measuring temperature changes down-gradient of subsurface structures is insufficient overall to assess thermal impacts, particularly in urban areas. Moreover, in areas which are densely urbanized, and where groundwater flow