Water suppliers face major challenges such as climate change and population growth. To prepare for the future, detailed knowledge of water resources is needed. In southern Germany, the state water supplier Zweckverband Landeswasserversorgung provides 3 million people with drinking water obtained from a complex karst and alluvial aquifer system and the river Danube. In this study, a combination of different tracing techniques was used with the goal of a multi-scale characterization of the aquifer system and to gain additional knowledge about groundwater flow toward the extraction wells in the Danube Valley. For the small-scale characterization, selected groundwater monitoring wells were examined using single-borehole dilution tests. With these tests, a wide range of flow behavior could be documented, including fast outflow within just a few hours in wells with good connection to the aquifer, but also durations of many weeks in low-permeability formations. Vertical flow, caused by multiple flow horizons or uprising groundwater, was detected in 40% of the tested wells. A regional multi-tracer test with three injections was used to investigate the aquifer on a large scale. For the highly karstified connection between a swallow hole and a spring group, high flow velocities of around 80 m/h could be documented. Exceptionally delayed arrivals, 250 and 307 days after the injection, respectively showing maximum velocities of 0.44 and 0.39 m/h, were observed in an area where low-permeability sediments overlay the karst conduits. With the chosen methods, a distinct heterogeneity caused by the geological setting could be documented on both scales.