The regulation of the world’s major river systems is threatening global biodiversity and generating the urgent need to manage river flows. One type of management is the delivery of restoration flows to regulated river systems. This is thought to help ecosystem recovery by mimicking a more natural flow regime and potentially restoring natural ecological processes and patterns. However, our understanding of the relationship between flow and ecological response is limited. Designing ecosystem-scale experiments and monitoring the delivery of restoration flows can help advance our knowledge of flow and ecological response. In this study, we carried out an ecosystem-scale experiment and manipulated flows in four managed rivers. One river received minimal flows (base flow), two rivers received natural flow pulses (natural flow) and one river received both natural flow pulses and the delivery of two restoration flows (restoration flow). We investigated whether changes in river flow regime can alter freshwater biodiversity in the Edward-Wakool river system, located in south eastern Australia. We sampled aquatic invertebrate communities on small woody debris over a seven-month period. We measured invertebrate abundance, biomass, taxonomic richness and community structure. We found invertebrate biomass to increase in the river which received restoration flows. For other invertebrate measures (taxonomic richness, abundance, composition) the restoration flow river was similar to the natural flow rivers and therefore seemed to mimic natural flow regimes. In summary, shifts in river flow regime can drive changes in invertebrate communities which may have consequences for higher trophic groups such as fish.