Despite the demonstrated utility of the Australian River Assessment Scheme (AUSRIVAS) to provide national-scale information on the biological condition of rivers, there is no commensurate scheme that can provide standardised information on physical habitat. Existing habitat assessment methods are not suitable for implementation on a national scale, so we present a new habitat assessment protocol that incorporates favorable elements of existing methods. Habitat Predictive Modelling forms the basis for the protocol because it can predict the occurrence of local-scale features from large-scale data, uses the reference condition concept, can be modified to incorporate a range of biologically and geomorphologically relevant variables, and employs a rapid survey approach. However, the protocol has been augmented with geomorphological variables and incorporates principles of hierarchy and geomorphological river zonation. There are four sequential components to the implementation of the protocol: reference site selection, data collection, predictive model construction and assessment of test sites using the predictive models. Once implemented, the habitat assessment protocol will provide a standardised tool for the assessment of river habitat condition at a variety of governance levels.