Anomalously high (up to +8°C) and low (−2°C) groundwater temperatures, as compared to undisturbed geothermal profiles, have been observed in unconsolidated siliciclastic aquifers off‐set by normal‐faults in the Lower Rhine Embayment, Germany. High hydraulic head gradients, induced by pumping, over the same faults suggest that they form effective barriers to lateral groundwater flow. Numerical analysis of the geothermal data presented here shows that the observed thermal anomalies can be explained under the assumption that the faults form a sub‐vertical pathway that is connecting deep and shallow aquifers that are elsewhere separated by confining units. The hydraulic head and temperature observations taken together are consistent with the hypothesis that these faults behave as a conduit‐barrier systems. Such behavior would arise from clay‐smearing and drag of sand along the fault plane. Most current models of fault hydrology in unconsolidated sedimentary sequences assume faults to be effective barriers to fluid flow. Therefore our findings can have important consequences for the assessment of contaminant flow or hydrocarbon migration in sedimentary aquifer systems cut by faults.