Environmental water is used to restore elements of the hydrological regime altered by human use of water, yet there has been little specific empirical evidence showing how river-floodplain trophic dynamics interact with hydrological regimes or research on incorporating food-web and trophic dynamics into the monitoring and evaluation of environmental flow programs. The Environmental Water and Knowledge Research (EWKR) program sets out to better understand the links between hydrology and aquatic food webs to inform the adaptive management of water in the Murray Darling Basin, Australia. We present a model conceptualising how hydrological regimes affect energy production and transfer in river-floodplain systems, and develop a generic framework for incorporating trophic dynamics into monitoring programs to identify the food-web linkages between hydrological regimes and population-level objectives of environmental flows. We identify key opportunities underway as part of the EWKR program for further research to enhance the conceptual basis and empirical knowledge underpinning trophic dynamics in river-floodplain systems. An improved understanding of how the hydrological regime influences spatial and temporal patterns of production and the movement of energy through river-floodplain networks is essential to determine whether the restoration of flow regimes through environmental flows will achieve targeted ecological outcomes for high-order consumers.