Weekly samples from surface waters, springs, soil water and rainfall were collected in a 76.9 km2 mountain rain forest catchment and its tributaries in southern Ecuador. Time series of the stable water isotopes δ18O and δ2H were used to calculate mean transit times (MTTs) and the transit time distribution functions (TTDs) solving the convolution method for seven lumped parameter models. For each model setup, the Generalized Likelihood Uncertainty Estimation (GLUE) methodology was applied to find the best predictions, behavioral solutions and parameter identifiability. For the study basin, TTDs based on model types such as the Linear-Piston Flow for soil waters and the Exponential-Piston Flow for surface waters and springs performed better than more versatile equations such as the Gamma and the Two Parallel Linear Reservoirs. Notwithstanding both approaches yielded a better goodness of fit for most sites, but with considerable larger uncertainty shown by GLUE. Among the tested models, corresponding results were obtained for soil waters with short MTTs (ranging from 3 to 12 weeks). For waters with longer MTTs differences were found, suggesting that for those cases the MTT should be based at least on an intercomparison of several models. Under dominant baseflow conditions long MTTs for stream water ≥2 yr were detected, a phenomenon also observed for shallow springs. Short MTTs for water in the top soil layer indicate a rapid exchange of surface waters with deeper soil horizons. Differences in travel times between soils suggest that there is evidence of a land use effect on flow generation.