The transit time (TT) of streamflow encapsulates information about how catchments store and release water and solutes of different ages. The young water fraction (Fyw), the fraction of streamflow that is younger than a certain age (normally 2–3 months), has been increasingly used as an alternative metric to the commonly used mean TT (mTT). In the commonly used (‘traditional’) procedure presented by Kirchner (2016), the age threshold (τyw) of Fyw separating young from old water is not pre-defined and differs from catchment to catchment depending on the shape of the (gamma) transit time distribution. However, it can be argued that it is important to use the same pre-defined τyw for inter-catchment comparison of Fyw. In this study, we propose an alternative (‘proposed’) procedure for the estimation of Fyw with any pre-defined τyw. This allows us to also compare the effects of data sampling frequencies on the results of Fyw estimation using the same τyw. We applied the traditional and proposed procedures using daily oxygen isotope (δ18O) data in the Alp and Erlenbach catchments, Switzerland. We found that our proposed and the traditional procedure can give very different Fyw values. With the proposed procedure, the estimated Fyw significantly increases when the sampling frequency changes from sub-monthly to monthly time steps. Overall, our study highlights the importance of the selection of τyw and the sampling frequency in Fyw estimation, which should be given more attention.