Abstract There is an increasing demand for tools to assist in the management of environmental flows in rivers. Changes in river discharge act on biota through a hydraulic template, which is mediated by channel morphology. Hence, environmental flow assessments also need to consider channel morphology, especially if morphology has been altered by human activities. Computer models describing the preferences of fish for hydraulic microhabitats have been applied to environmental flow problems since the mid-1970s. Salmonids have been a particular focus for these methods. Other reviews have provided comprehensive coverage of the basic features and principles of such models. These are briefly discussed focusing on the developments that have occurred in the last 15 years and whose application has so far been infrequent. These include improvements to the representation of hydraulics at reach-scale and of longer river sections, and improved representation of interacting physical variables that describe habitat. The central theme is the spatial coverage and fundamental granularity of such models. Despite a broad literature, there is a lack of documented examples of the application of hydraulic-habitat models through all stages in the environmental flow decision-making process. The review concludes with four short examples that illustrate the use of model output.