The exchange of energy (carbon) and nutrients is a primary characteristic which controls productivity and community dynamics in riverine systems. These exchanges, in managed ecosystems, are controlled and decided based on balancing the needs of agriculture, society, and ecology. Maintaining ecological status and promoting keynote species (i.e. Murray Cod, Maccullochella peelii) requires underlying knowledge of the food web and carbon delivery pathways that deliver the required nutrients at the correct time. By examining the linkages between consumers and resources within a community, we can propose management decisions which support keynote species and their underlying food webs, while balancing the needs of agriculture and society. The aim is to develop sophisticated understanding of the ecological response to flow and to use this information to assess the likely responses to various operation scenarios. A floodplain system in the Lower River Murray was sampled in two consecutive years for to characterize the food web which supports Murray Cod larvae survival. Natural abundances of δ13C and δ15N were measured from all trophic levels to provide integrated measures of assimilation and partitioning of the relative contributions of basal carbon sources to food webs to trace patterns of energy flow and food web linkages in ecosystem. We demonstrate distinct trophic interactions within discrete morphological areas of the floodplain, propose how inundation events will alter the fate of energy and nutrients, and the likely resulting ecological response.