Many Australian river ecosystems have been, and continue to be, adversely affected by increased channel dimensions and sediment supplies occurring in the period since European settlement. One of the key aims of river rehabilitation in these rivers is to help reduce sediment yield by preventing ongoing bank erosion and remobilization of instream bed material stores. While various tools have been developed to help identify sediment sources at the catchment scale, this is often at a resolution that is too coarse to be translated directly to on-ground rehabilitation works, as most riverworks programs are designed and implemented at the reach or within-reach scale. This paper provides a method of prioritizing rehabilitation at the within-reach scale by using a high-resolution reach-scale modelling approach to examine the relative entrainment potential of sediment stores. The method has been developed for a 10 km reach of the upper Hunter River, NSW, Australia. Shear stress distribution is examined using the widely available model HEC-RAS, and incorporating a detailed, LiDAR-derived, representation of the in-channel vegetation into a spatially distributed Manning's roughness layer. At the geomorphic unit scale, the results highlight that the elevated ‘bench’ units, which represent significant stores of sand and silt, are much more vulnerable to remobilization than the lower elevation gravel bar units. At the sub-reach scale (500–2000 m) shear stresses are greatest in the most confined sections. While instream geomorphic heterogeneity has been significantly reduced in these locations, ongoing erosion is limited by bedrock and buried coarse gravel terrace material in the bed and banks. These results highlight the need for targeted rehabilitation strategies that account for within-reach variability in entrainment potential as well as on-the-ground knowledge of sediment supply and geological controls. Copyright © 2010 John Wiley & Sons, Ltd.