River landscapes are increasingly viewed as a collection of nested geomorphic features, the hydrological effects of which juxtapose to create a mosaic of aquatic habitat conditions. We examined how the combined hydrological influences of stream reaches and gravel bars affect the composition of hyporheic invertebrate assemblages along the longitudinal and vertical dimensions of river landscapes. We worked in 12 braided-river valley segments of tributaries to the Rhône River, France. Valley segments were bounded downstream by geological knickpoints so that bedform-induced exchange flows beneath gravel bars and riffles were predictably embedded in exchange flows occurring at the valley-segment scale. In upstream reaches (UR) and downstream reaches (DR) of each valley segment, we collected invertebrates at the heads and tails of gravel bars in the hyporheic zone and at the upstream and downstream ends of riffles in surface channels adjacent to the bars. Patterns of vertical hydraulic gradient and specific conductance and the resulting spatial heterogeneity of temperature, dissolved O₂, and particulate organic C suggested that DR were points of flow convergence and water mixing. Specific conductance increased and temperature decreased more steeply along gravel bars in DR, indicating that water from long hyporheic flow paths or lateral aquifers was discharging at the tails of bars in DR. Density hotspots for insect larvae corresponded to hyporheic patches at the heads of bars in DR, which received the highest organic matter inputs from localized downwelling of surface water and were not affected by inputs of cold water from hyporheic flow paths or lateral aquifers. Density of epigean taxa at the tails of bars decreased more steeply with depth in DR than in UR, and density of hypogean taxa increased more steeply. Viewing local hyporheic assemblages as the outcome of a series of environmental filters operating over multiple exchange flows induced by nested geomorphic features provides a general framework that may foster our understanding of biodiversity patterns in river landscapes.