The hydrogeology, runoff generation and water quality generation in old peneplains of Central Europe built by acid crystalline rocks (such as the Bohemo-Moravian Highland) are described and interpreted in terms of a three-zone concept. The recharge zones are located on flat tops of hills and their soils are mostly permeable. It is mainly through them that the shallow groundwater-bearing formations are loaded with nitrate. The groundwater exfiltrates on the lower parts of slopes (in the so-called transient zone) and in narrow valleys (in the discharge zone), creating dispersed springs and waterlogged areas. In addition, the rapid and shallow flow of perched groundwater down the slope, which takes place during wet periods in the recharge zone and, mainly, in the transient zone, leaches the nitrate from the soil directly to the stream, without necessarily being in contact with the permanent groundwater table of the recharge and the transient zones. Discharge and water quality measurements in the Kopaninský tok experimental catchment (6.7 km 2) were analysed, using a combination of two runoff separation techniques (a digital filter and a simple conceptual model GROUND). Three runoff components were distinguished (direct runoff, interflow and baseflow). There is a weak but significant positive correlation between the stream nitrate concentration on the one hand and either the interflow or the baseflow on the other hand. There is also a weak but significant negative correlation between the stream nitrate concentration on the one hand and either the ratio of direct runoff to total stream flow or the logarithm of this ratio on the other hand, provided that the cases of zero direct runoff are disregarded. A simple mixing model was used to estimate the characteristic nitrate concentrations of individual runoff components. The interflow has the highest characteristic nitrate concentration and is probably the main stream water polluter with nitrate. The baseflow is identified as the likely second main polluter. The differences in water quality between a drainage outlet and a forest spring indicate the importance of a proper nitrogen management in the recharge zones. It is also concluded that the tile drainage and tillage of formerly waterlogged sites, mainly located in transient zones, reduce the opportunity for denitrification of both baseflow and interflow. The ploughed lands in the recharge zones represent an established basis for local agriculture and cannot be easily set aside. Many such lands have been declared as vulnerable to nitrate pollution in order to protect waters against impacts of risky agricultural practices. It is proposed that some waterlogged and drained sites in the transient and discharge zones are set aside rather than the flat ploughed lands on the hill tops. To increase the denitrification, tile drainage runoff from the transient and the discharge zones should be retarded.