Mountains in general are important sources of water resources and correspondingly, the Upper Indus Basin (UIB) in the Himalayas provides water for hundreds of millions of users. During low-flow periods, streamflow is fed by a combination of groundwater (baseflow), snow/glacier melt and recent precipitation. However, the proportion of stream baseflow generated by different sources and the factors that control these contributions remain poorly understood. In this paper, we focus on the Western Himalayan Liddar watershed (1243 km2) in the UIB and use a multi-method approach to characterize aquifers and baseflow generation in three nested catchments which represent varying geology and topography. Our multi-method approach includes geophysical surveys, slug tests, stable isotope compositions, young water fraction (Fyw) estimation and a Bayesian end member mixing model. Specifically, we hypothesize that Ksat of the subsurface plays a critical role in the contribution of groundwater to baseflow. The watershed is subdivided into three nested catchments (Limestone, hardrock and alluvium). Our results indicate that the upstream, steep, high-permeability limestone catchment has the relatively largest groundwater contribution to streamflow (63–78 %) and a low Fyw (38 %) than the other two sites. The mid-elevation hard rock catchment has a lower permeability on average but is highly variable due to fracture networks and geologic contacts, allowing a substantial groundwater contribution to streamflow (38–66 %) and a similar Fyw (36 %) to the limestone catchment. The downstream, low-slope catchment underlain by alluvium has a highly variable hydraulic conductivity and a substantially lower groundwater contribution to streamflow (26–45 %) and a higher Fyw (55 %). We find that both hydraulic conductivity and topography exert control on the magnitude of baseflow contribution to the stream. However, Ksat acts as a key control in groundwater contribution to baseflow as observed in headwaters and downstream region of the watershed. While unconsolidated deposits are often thought of as important high-porosity mountain aquifers, our results point to the importance of fractured and karstified bedrock in baseflow generation in high mountains. As climate change alters the snow- and ice-melt regimes of UIB rivers, our study underscores the critical importance of improving our understanding of baseflow sources.