The maintenance of ecological health in rivers by flow management has been a focus of debate for many years. The role of bed load transport and stability of substrate has long been recognised as an integral part of that management. However, there are few effective methods that have been developed to successfully evaluate and quantify this link. Quantifying the relationship between benthic communities and substrate stability offers the potential to effectively manage benthic community composition to maintain ecological condition. Substrate stability is the result of a complex set of interactions operating over a range of spatial and temporal scales. Direct measurement of these processes can be difficult and time consuming. A number of indices and methodologies to assess this have been developed to provide a quick and accurate assessment of substrate stability, but have produced poor results to date. This paper will introduce some new bed stability measures that offer considerable promise to measure quickly and effectively at the scale necessary to truly reflect ecological conditions for benthic biota.