The Environmental Watering Knowledge and Research (EWKR) project is interested in the influence of flows on floodplain food webs, and incorporates existing information with new research to address knowledge gaps. The Food Web theme leadership group of EWKR has identified that the relationship between environmental flows and the provisioning of resources for plants and animals remains a critical knowledge gap in the Murray–Darling Basin. The Flood Pulse Concept conceived by Junk et al. highlights the importance of riverine–floodplain interaction in influencing character and condition. While developed within the context of a tropical basin, it has been broadly applied to diverse rivers around the world. Despite recognition of its importance, very few studies have provided empirical evidence to support a number of its hypotheses. Here we discuss results from an existing project that will contribute to research as part of the EWKR Food Web theme. The project discussed investigates the biological responses of ephemeral wetlands to a manipulated flood pulse. We compared and contrasted water quality, nutrient and macroinvertebrate community data, collected over a 22–week inundation period, between ephemeral and permanent floodplain wetlands. Ephemeral wetlands supported different aquatic macroinvertebrate communities to permanent wetlands and this was largely driven by differences in water quality and nutrient concentrations. Taxa richness and diversity was higher at permanent wetlands while ephemeral wetlands supported greater macroinvertebrate abundance and biomass. Community differences between hydrological treatments were driven primarily by Chironomidae, while early colonising Coleoptera contributed strongly to taxa richness in ephemeral wetlands. Chironmus tepperi was the dominant taxon among ephemeral wetlands, both numerically and by biomass. Analysis of functional feeding groups (FFG) indicated that ephemeral wetlands contained a higher proportion of detrital feeding collector–gatherers compared to permanent wetlands, suggesting an increased reliance on heterotrophic energy pathways. Here we show that a manipulated flood pulse mimicking a natural flood can mobilise latent terrestrial energy sources within ephemeral floodplain wetlands and support a boom of aquatic invertebrate biomass with important implications for both terrestrial and aquatic food webs. These results contribute to our knowledge of the effects of environmental flows on the passage of energy through floodplain food webs and provide managers with useful information about abiotic and biotic responses of ephemeral floodplain wetlands following a manipulated flood pulse.