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Rivers transfer particulate organic carbon (POC) from eroding mountains into geological sinks. Organic carbon source composition and selective mobilization have been shown to affect the type and quantity of POC export, but their combined effects across complex mountain ranges remain underexplored. Here, we examine the variation in organic carbon sourcing and transport in the trans-Himalayan Kali Gandaki River catchment, along strong gradients in precipitation, rock type and vegetation. Combining bulk stable nitrogen, and stable and radioactive organic carbon isotopic composition of bedrock, litter, soil and river sediment samples with a Bayesian end-member mixing approach, we differentiate POC sources along the river and quantify their export. Our analysis shows that POC export from the Tibetan segment of the catchment, where carbon bearing shales are partially covered by aged and modern soils, is dominated by petrogenic POC. Based on our data we re-assess the presence of aged biospheric OC in this part of the catchment, and its contribution to the river load. In the High Himalayan segment, we observed low inputs of petrogenic and biospheric POC, likely due to very low organic carbon concentrations in the metamorphic bedrock, combined with erosion dominated by deep-seated landslides. Our findings show that along the Kali Gandaki River, the sourcing of sediment and organic carbon are decoupled, due to differences in rock organic carbon content, soil and above ground carbon stocks, and geomorphic process activity. While the fast eroding High Himalayas are the principal source of river sediment, the Tibetan headwaters, where erosion rates are lower, are the principal source of organic carbon. To robustly estimate organic carbon export from the Himalayas, the mountain range should be divided into tectono-physiographic zones with distinct organic carbon yields due to differences in substrate and erosion processes and rates.