Abstract Whilst flow is often seen simplistically as a measurable and manageable variable in rivers, the habitat value of flow is delivered by interactions with channel morphology and substrate. The resulting hydromorphology impacts on all salmonid life stages; its proper understanding requires integration between the sciences of hydrology/hydraulics, geomorphology and freshwater ecology, but this integration is scarce. This study describes those features of river channel morphology and dynamics that are most relevant to hydromorphological status, describes progress in field assessment and outlines practical progress in calibrating in-channel habitat condition as an aid to setting flows. However, the incorporation of the true spatial and temporal variability of hydromorphology awaits further refinement of survey techniques and the long-awaited interdisciplinary research on causal process links. Meanwhile, amongst the geomorphological tools available to those setting environmental flows are fluvial audits, the definition and mapping of meso-scale biotopes and the use of realistic river typologies for the local application of general flow rules.