The temporal dynamics and geographical sources of streamflow were conceptualized in a lumped rainfall-runoff model (isoSAMdyn) using isotopic and geochemical tracers derived from a field study in a 3.6 km2 upland catchment in Scotland. High-resolution (daily) sampling of stable isotopes in precipitation and streamflow over a hydrological year, supplemented by fortnightly sampling of groundwater and riparian saturation zones, allowed hypotheses of runoff generation processes to be tested. These were conceptualized in a previously developed model (SAMdyn) based only on geochemically defined geographic source tracers, which showed that the nonlinear dynamic expansion and contraction of riparian saturation areas is the dominant mechanism for storm runoff generation in the catchment. While SAMdyn resulted in reasonable simulation of streamflows and alkalinity (as a source tracer), it was unable to reproduce the rainfall-runoff dynamics of deuterium (δ2H). Using the model in a learning framework, incorporation of parameters for passive storage in catchment hillslopes and groundwater mixing in riparian saturation zones, along with associated isotopic fractionation, improved δ2H simulations in stream water and the major catchment water stores. The resulting model provided a conceptualization of rainfall-runoff processes that broadly reconciled hydrometric data and geochemical and isotopic signals. However, in this particular catchment, fractionation of water in surface saturation zones appears to be a complex process that prevents the simulation of short-term isotope dynamics in the stream during the summer period.