Preferential flow paths in hydrological systems (e.g., macropores or subsurface pipe networks) facilitate rapid water and solute transport, leading to fast streamflow responses and markedly short transit times. While such preferential flow processes are well known in the unsaturated zone and groundwater, it remains uncertain whether catchment-scale isotope-based transport models can accurately represent these fast groundwater flow processes. In this study, we tested the hypothesis that preferential discharge of young groundwater is significant and can be captured by selecting specific StorAge Selection (SAS) functions, i.e., functions that specify if young or old water leaves a storage, at the catchment scale. We systematically compared multiple SAS parameterisations for the unsaturated zone and groundwater using a catchment scale transport model and long-term measurements of hydrogen isotopes (δ<sup>2</sup>H) data from two headwater catchments (Hydrological Open Air Laboratory, HOAL, catchment in Austria and Wüstebach catchment in Germany). The results indicated that δ<sup>2</sup>H ratios in streamflow had sufficient information content to identify preferential flow in the unsaturated zone. However, δ<sup>2</sup>H ratios in streamflow were insufficient to constrain or confirm preferential flow in groundwater, as any seasonal variation of δ<sup>2</sup>H in pore water was largely dampened by the catchments’ substantial passive groundwater storage volumes. This was further confirmed as the observed attenuated δ<sup>2</sup>H signal in streamflow could only be simulated when the volume ratio between active and passive groundwater storage was < 1 %. This damping effect affected the estimation of the longer tails (100 < <em>T</em> < 1000 days) of the transit time distributions, making it challenging to estimate how much of the streamwater actually is older than 100 days. In addition, weekly resolution δ<sup>2</sup>H measurements led to deceptively high-performance metrics (e.g., Nash–Sutcliffe Efficiency), even when key model parameters for groundwater age selection —such as young- versus old-water selection preferences—remain poorly constrained. As a result, the variation in the estimation of the fraction of stream water younger than 1000 days was approximately 20 % in the HOAL and 23 % in the Wüstebach catchments due to the SAS function shape holding similar model performance. These findings underscore the need for complementary data sources, such as multiple tracers, high-frequency sampling, or groundwater-level monitoring, to better constrain preferential flow processes and to reduce uncertainty in catchment-scale water transit time modelling.