Context. Environmental water is often used to manage floodplain wetlands that support many taxa, both terrestrial and aquatic. It is important to optimise the managed hydroperiod to maximise the provision of aquatically derived resources from wetlands. Aims. To test the hypothesis that increasing hydroperiod affects food-web structure and energy production in floodplain wetlands. Methods. Fatty acids and stable isotopes of δ13C and δ15N were used to define food-web structure, and estimate total energy production throughout a managed inundation event in a wetland in the northern Murray–Darling Basin. Key results. Food-web complexity increased with an increasing hydroperiod in line with predictable patterns of community assemblage development, before reducing sharply immediately prior to drying. Energy availability increased with an increasing hydroperiod and there was a strong correlation (ρ = 0.669, P = 0.0001) between energy availability and fatty acid concentration, which was in turn related to patterns of taxon occurrence. Conclusions and implications. Hydroperiod exerts a strong influence on aquatic invertebrate community trophic dynamics and energy provision. Planned flows should support maturation and stabilisation of the invertebrate community to optimise energy provision to consumers.