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1. The chemical characteristics of floodwaters in ephemeral rivers are little known, particularly with regard to their organic loads. These rivers typically exhibit a pronounced downstream hydrological decay but few studies have documented its effect on chemical characteristics and material transport. To develop a better understanding of the dynamics of floods and associated material transport in large ephemeral rivers, floods of the ephemeral Kuiseb River in south-western Africa were tracked and repeatedly sampled at multiple points along the river’s lower 220 km.

2. We quantified the composition and transport of solute and sediment loads in relation to longitudinal hydrological patterns associated with downstream hydrological decay. Source and sink areas for transported materials were identified, and the composition and transport dynamics of the organic matter load were compared to those described from more mesic systems.

3. Concentrations of sediments and solutes transported by floods in the Kuiseb River tended to increase downstream in association with pronounced hydrological decay. The contribution of particulate organic matter to total organic load is among the highest recorded, despite our observation of unusually high levels of dissolved organic matter. Hydrological decay resulted in deposition of all transported material within the lower Kuiseb River, with no discharge of water or materials to the Atlantic Ocean.

4. Our results suggest that longitudinal variation in surface flow and associated patterns of material transport renders the lower Kuiseb River a sink for materials transported from upstream. The downstream transport and deposition of large amounts of labile organic matter provides an important carbon supplement to heterotrophic communities within the river’s lower reaches.