An important quantity in groundwater protection is the residence time of water in an aquifer. It relates to both the travel time of a pollutant to arrive at a well and the time span required for self-purification of a polluted aquifer after removal of pollutant inputs. Time scales for aquifers can be gained from artificial tracer experiments or from environmental tracer data, the latter offering the only realistic alternative if time scales of years or decades have to be taken into account. Different tracers show different time scales due to their different transport mechanisms especially in the unsaturated zone. While solute tracers are moved advectively with the seepage water, gas tracers pass the unsaturated zone diffusively through the air phase. Depending on the properties of the unsaturated zone (hydraulic properties, thickness) this difference in behavior can be used to separate the subsurface transport process into the unsaturated and the saturated parts. In a field study in Germany, SF 6 and 3H were used as environmental tracers. Both have a relatively well-known input function. Interpretation of data from observation wells by a box model approach led to spatially and temporally varying residence times. This was an indication that the influence of the unsaturated zone could not be neglected. While the gas tracer SF 6 shows only residence times in the saturated zone, the tracer 3H reflects the whole travel time of water including both the unsaturated and saturated zones. Using a one-dimensional plug-flow model for the unsaturated zone combined with a detailed two-dimensional flow and transport model for the saturated zone leads to a holistic and consistent interpretation of the measured tracer concentrations. The observed pattern of old water under thick loess cover and younger water under areas where the fractured basalt aquifer crops out is reproduced after adjusting only two parameters: the effective porosity of the saturated aquifer and the product of field capacity and thickness of the unsaturated zone. While the effective porosity of the saturated zone is adjusted by means of the SF 6 data, the field capacity of the loess layer is adjusted by means of the 3H observations. The thickness of the unsaturated zone is deduced from geological and pedological maps. All flow data are obtained from a calibrated flow model, which is based on geological data, observed heads and pumping tests only. The transport model for the saturated zone was calibrated by fitting the porosity by means of gaseous tracer concentrations (SF 6). The combined saturated–unsaturated zone model was then calibrated by fitting the field capacity of the unsaturated zone by means of 3H concentrations. With this model it was possible to verify the observed NO 3 concentrations at the drinking water wells and to develop predictions for their future development under various scenarios of fertilizer input reduction in specific areas.