We propose that the mechanisms driving hyporheic exchange vary systematically with different channel morphologies and associated fluvial processes that occur in mountain basins, providing a framework for examining physical controls on hyporheic environments and their spatial variation across the landscape. Furthermore, the spatial distribution of hyporheic environments within mountain catchments represents a nested hierarchy of process controls. Large-scale process drivers (geology, climate, fire, and land use) impose a suite of watershed conditions (topography, streamflow, sediment supply, and vegetation) on the fluvial system. Different combinations of imposed watershed conditions result in different reach-scale channel morphologies (e.g. step-pool, pool-riffle, and braided) that, in turn, structure hyporheic processes (e.g. pressure divergence, spatial variation of hydraulic conductivity) and resultant hyporheic environments (scales and rates of hyporheic exchange). Consequently, a holistic view of natural and anthropogenic drivers over a range of spatial and temporal scales is needed for understanding hyporheic ecosystems.