In continental rift zones, thermal anomalies and enhanced occurrence of mantle-derived fluids in groundwaters often coincide on a continental but rarely on the local scale. For areas of recent intraplate volcanism this suggests a time shift between the transport of mantle-derived volatiles and heat to the Earth's surface. As a particularly illustrative example, we studied the central European Rhine graben, which is distinguished by extensional tectonics, high seismicity, young, Upper Tertiary volcanism, abundant mineral water springs, and a heat flow anomaly. A combination of thermal, helium isotope, and major element data of mineral waters with numerical simulations of flow and heat transport leads to a profound understanding of crustal-scale transport processes and allows a clear distinction between diffusion and flow dominated regimes. The simulations show that for a crustal-scale system the transition between these two regimes occurs within one decade of permeability (10-16--10-17 m2). Flow is likely to be strongly controlled by fault systems both in the lower and upper crust. While thermal anomalies highlight fluid circulation within the upper brittle crust, mantle-derived volatiles provide information on transport phenomena from lower crustal sections. The thermal and hydro-chemical anomalies in the Upper Rhine graben are directly related to mass flow rates. Therefore lack of thermal anomalies around the Kaiserstuhl volcano suggests that mass flow rates must be very small, while positive thermal anomalies in the central part of the graben can directly be related to advection of fluids into basin sediments and to redistribution of heat within these sediments.