The vertical structure of river beds varies temporally and spatially in response to hydraulic regime, sediment mobility, grain size distribution and faunal interaction. Implicit are changes to the active layer depth and bed porosity, both critical in describing processes such as armour layer development, surface-subsurface exchange processes and siltation/sealing. Whilst measurements of the bed surface are increasingly informed by quantitative and spatial measurement techniques (e.g. laser displacement scanning), material opacity has precluded the full 3-D bed structure analysis required to accurately define the surface-subsurface transition. To overcome this problem, this paper provides Magnetic Resonance Imaging data of vertical bed porosity profiles. Uniform and bimodal (sg = 2.1) sand-gravel beds are considered following restructuring under sub-threshold flow durations of 60 and 960 minutes. MRI data are compared to traditional 2.5-D laser displacement scans and six robust definitions of the surface-subsurface transition are provided; these form the focus of discussion.