River health assessments traditionally focus on water quantity, water quality metrics and/or biological indicators such as fish and birds. While valuable, these approaches can overlook the energetic processes that underpin aquatic food webs and population level response. The Flow-MER Water Packet Poker project contributes to closing this gap by investigating functional indicators that describe the quantity and quality of basal resources and lower trophic levels supporting river productivity across the Murray-Darling Basin. The project aims to characterise spatial and temporal variation in standardised, rapidly sampled indicators associated with ecosystem function, including dissolved organic carbon, dissolved organic matter quality, nutrient concentrations, chlorophyll-a, and seston quantity and quality. We hypothesise that flow regime and floodplain connectivity are major drivers of energy availability and thus food-web dynamics. A pilot study in the southern Basin, across regulated and unregulated reaches of the Murray, Kiewa and Ovens rivers, captured contrasting hydrological conditions. Preliminary results indicate substantial variability in resource quantity and quality among systems, highlighting the influence of flow and river regulation on resource availability. We advocate developing a Basin-scale understanding of how water source influences food-web resources, which will provide managers with improved knowledge to predict ecological outcomes of environmental flows and anticipate risks such as hypoxia and algal blooms.