The transit time of water is an important indicator of catchment functioning and affects many biological and geochemical processes. Water entering a catchment at one point in time is composed of water molecules that will spend different amounts of time in the catchment before exiting. The next water input pulse can exhibit a totally different distribution of transit times. The distribution of water transit times is thus best characterized by a time-variable probability density function. It is often assumed, however, that the variability of the transit time distribution is negligible and that catchments can be characterized with a unique transit time distribution. In many cases this assumption is not valid because of variations in precipitation, evapotranspiration, and catchment water storage and associated (de) activation of dominant flow paths. This paper presents a general method to estimate the time-variable transit time distribution of catchment waters. Application of the method using several years of rainfall-runoff and stable water isotope data yields an ensemble of transit time distributions with different moments. The combined probability density function represents the master transit time distribution and characterizes the intra-annual and interannual variability of catchment storage and flow paths. Comparing the derived master transit time distributions of two research catchments (one humid and one semiarid) reveals differences in dominant hydrologic processes and dynamic water storage behavior, with the semiarid catchment generally reacting slower to precipitation events and containing a lower fraction of preevent water in the immediate hydrologic response.