The Murray Darling Basin Environmental Watering and Knowledge Research project aims to address Basin-wide research questions and knowledge gaps. The relationship between environmental flows and the provision of resources across life stages of plants and animals has been identified as a critical knowledge gap in the Murray–Darling Basin. Understanding trophic interactions in riverine food webs is essential for predicting ecosystem responses and improving management decisions. Flow is known to influence the amount and type of organic matter available to food webs, and is thought to be a primary driver of the recruitment of fish and waterbirds. Understanding which basal resources are supporting fish and waterbird recruitment will enable identification of specific habitats and flow characteristics that will deliver the resources required to support or enhance recruitment. We seek to identify critical basal resources supporting fish recruitment and aim to trace the flow of energy through riverine ecosystems. Stable isotope composition and fatty acid profiles of material from a range of compartments within food webs of wetlands, anabranches and river channels was determined. We present empirical data that expresses relative magnitudes of energy pathways to taxa of interest and provide information to inform and refine new and existing models.