Hyporheic exchange flow (HEF) at the streambed–water interface (SWI) has been shown to impact the pattern and rate of discharging groundwater flow (GWF) and the consequential transport of heat, solutes and contaminants from the subsurface into streams. However, the control of geographic and hydromorphological catchment characteristics on GWF–HEF interactions is still not fully understood. Here, the spatial variability in flow characteristics in discharge zones was investigated and averaged over three spatial scales in five geographically different catchments in Sweden. Specifically, the deep GWF discharge velocity at the SWI was estimated using steady-state numerical models, accounting for the real multiscale topography and heterogeneous geology, while an analytical model, based on power spectral analysis of the streambed topography and statistical assessments of the stream hydraulics, was used to estimate the HEF. The modeling resulted in large variability in deep GWF and HEF velocities, both within and between catchments, and a regression analysis was performed to explain this observed variability by using a set of independent variables representing catchment topography and geology as well as local stream hydromorphology. Moreover, the HEF velocity was approximately two orders of magnitude larger than the deep GWF velocity in most of the investigated stream reaches, indicating significant potential to accelerate the deep GWF velocity and reduce the discharge areas. The greatest impact occurred in catchments with low average slope and in reaches close to the catchment outlet, where the deep GWF discharge velocity was generally low.