Environmental flows are managed events in river systems designed to enhance the ecological condition of aquatic ecosystems. Although not traditionally seen as important in lowland rivers, there is mounting evidence that terrestrial subsidies can be an important energy source in aquatic metazoan food webs. We argue that the apparent lack of importance of terrestrial subsidies to many lowland river food webs may reflect an artefact resulting from historical anthropogenic changes to lowland river-floodplain ecosystems, including the loss of lateral connectivity between rivers and their floodplains, changes in floodplain land use and carbon stores, and loss of sites of transformation within the main channel. The loss of floodplain subsidies to the main river channel can be partially redressed using environmental flows; however, this will require mimicking important aspects of natural high-flow events that have hitherto been overlooked when targeting environmental flows to a limited suite of biota. We suggest that key biotic targets for environmental flow releases may not be achievable unless river-floodplain subsidies are sufficiently restored. Environmental flows can go some way to addressing this shortfall, but only if floodplain subsidies to river channels are explicitly included in the design and management of environmental flows.