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Confluences are nodes in riverine networks characterized by complex three-dimensional changes in flow hydrodynamics and riverbed morphology, and are valued for important ecological functions. This physical complexity is often investigated within the water column or riverbed, while few studies have focused on hyporheic fluxes, which is the mixing of surface water and groundwater across the riverbed. This study aims to understand how hyporheic flux across the riverbed is organized by confluence physical drivers. Field investigations were carried out at a low gradient, headwater confluence between Baltimore Brook and Cold Brook in Marcellus, New York, USA. The study measured channel bathymetry, hydraulic permeability, and vertical temperature profiles, as indicators of the hyporheic exchange due to temperature gradients. Confluence geometry, hydrodynamics, and morphodynamics were found to significantly affect hyporheic exchange rate and patterns. Local scale bed morphology, such as the confluence scour hole and minor topographic irregularities, influenced the distribution of bed pressure head and the related patterns of downwelling/upwelling. Furthermore, classical back-to-back bend planform and the related secondary circulation probably affected hyporheic exchange patterns around the confluence shear layer. Finally, even variations in the hydrological conditions played a role on hyporheic fluxes modifying confluence planform, and, in turn, flow circulation patterns.