Following more than a decade of environmental flow delivery the assumptions underlying relationships between managed flows and physical habitat have rarely been tested. Improved understanding of flow-habitat relationships will lead to more informed water management and improve our understanding of the mechanistic relationship between hydrologic change and biotic response. We quantified the relationship between environmental flows and physical habitat, namely the availability of slackwaters and deepwater habitat, and the extent to which coarse-grained substrate sediments are smothered by deposited suspended sediment. Relationships were developed from intensive field sampling in the Goulburn River, Australia, and comparisons with the flow regime, specifically flow freshes and baseflows, such as those delivered by the Commonwealth Environmental Water Holder. We found that slackwaters are increased by baseflows but reduced by flow freshes, whereas deepwater habitat is universally increased by environmental flows. The relationship between flows and sediment smothering, however, is considerably more variable spatially and temporally, and antecedent conditions (both managed and natural) play an important role. The results demonstrate the importance of understanding responses of physical habitat to flow as the desired influence is not always as expected. These findings and the relationships developed will assist water managers to better demonstrate the influence of managed flows and assist operations to be tailored to desired outcomes.