1.  River corridors can be visualised as a three‐dimensional mosaic of surface–subsurface exchange patches over multiple spatial scales. Along major flow paths, surface water downwells into the sediment, travels for some distance beneath or along the stream, eventually mixes with ground water, and then returns to the stream. 2.  Spatial variations in bed topography and sediment permeability result in a mosaic of patch types (e.g. gravel versus sandy patches) that differ in their hydrological exchange rate with the surface stream. Biogeochemical processes and invertebrate assemblages vary among patch types as a function of the flux of advected channel water that determines the supply of organic matter and terminal electron acceptors. 3.  The overall effect of surface–subsurface hydrological exchanges on nutrient cycling and biodiversity in streams not only depends on the proportion of the different patch types, but also on the frequency distribution of patch size and shape. 4.  Because nutrients are essentially produced or depleted at the downwelling end of hyporheic flow paths, reach‐scale processing rates of nutrients should be greater in stretches with many small patches (e.g. short compact gravel bars) than in stretches with only a few large patches (e.g. large gravel bars). 5.  Based on data from the Rhône River, we predict that a reach with many small bars should offer more hyporheic refugia for epigean fauna than a reach containing only a few large gravel bars because benthic organisms accumulate preferentially in sediments located at the upstream and downwelling edge of bars during floods. However, large bars are more stable and may provide the only refugia during severe flood events. 6.  In river floodplain systems exhibiting pronounced expansion/contraction cycles, hyporheic assemblages within newly created patches not only depend on the intrinsic characteristics of these patches but also on their life span, hydrological connection with neighbouring patches, and movement patterns of organisms. 7.  Empirical and theoretical evidence illustrate how the spatial arrangement of surface–subsurface exchange patches affects heterogeneity in stream nutrient concentration, surface water temperature, and colonisation of dry reaches by invertebrates. 8.  Interactions between fluvial action and geomorphic features, resulting from seasonal and episodic flow pulses, alter surface–subsurface exchange pathways and repeatedly modify the configuration of the mosaic, thereby altering the contribution of the hyporheic zone to nutrient transformation and biodiversity in river corridors.

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