AbstractBy use of numerical modeling and field observations, this work quantified the effects of catchment‐scale upwelling groundwater on the hyporheic (below stream) fluxes over a wide range of spatial scales. A groundwater flow model was developed that specifically accounted for the hydrostatic and dynamic head fluctuations induced by the streambed topography. Although the magnitudes and relative importance of these streambed‐induced fluxes were found to be highly sensitive to site‐specific hydromorphological properties, we showed that streambed topographic structures exert a predominant control on the magnitude of hyporheic exchange fluxes in a Swedish boreal catchment. The magnitude of the exchange intensity evaluated at the streambed interface was found to be dominated by the streambed‐induced hydraulic head across stream order. However, the catchment‐scale groundwater flow field substantially affected the distribution of groundwater discharge points and thus decreased the fragmentation of the hyporheic zone, specifically by shifting the cumulative density function toward larger areas of coherent upwelling at the streambed interface. This work highlights the spectrum of spatial scales affecting the surface water‐groundwater exchange patterns and resolves the roles of key mechanisms in controlling the fragmentation of the hyporheic zone.