Hydrological monitoring in small headwater catchments provides the basis for examining complex interrelating hydraulic processes that govern the runoff generation. Contributions of different subsurface runoff mechanisms to the catchment discharge formation at two small forested headwater catchments are studied with the help of their natural isotopic signatures. The Uhlirska catchment (Jizera Mts., Czech Republic) is situated in headwater area of the Lusatian Neisse River. The catchment includes wetlands at the valley bottom developed over deluviofluvial granitic sediments surrounded by gentle hillslopes with shallow soils underlain by weathered granite. The Liz catchment (Bohemian Forest, Czech Republic) is situated in headwater area of the Otava River. It belongs to hillslope-type catchments with narrow riparian zones. The soil at Liz is developed on biotite paragneiss bedrock. The basic comparison of hydrological time series reveals that the event-related stream discharge variations at the Uhlirska catchment are bigger and significantly more frequent than at Liz. The analysis of isotope concentration data revealed different behavior of the two catchments during the major rainfall-runoff events. At Uhlirska, the percentage of the direct runoff formed by the event water reaches its maximum on the falling limb of the hydrograph. At Liz, the event water related fraction of the direct outflow is maximal on the rising limb of the hydrograph and then lowers. The hydraulic functioning of the Uhlirska catchment is determined by communication between hillslope and riparian zone compartments.