We examined the effects of wetland inundation on three groups of aquatic invertebrates, including benthic and pelagic invertebrates and macroinvertebrates, in wetlands on the Gwydir River system in the north of the Murray-Darling Basin. We hypothesised that wetlands that were inundated for longer periods of time would support a greater richness and abundance of invertebrates, thus altering their assemblage structures. We chose four sites in each of two wetland systems, the Gingham Channel the Lower Gwydir Channel. Invertebrates were sampled seasonally on twenty sampling occasions between 2014 and 2019. Inundation was calculated as time since connection of the wetlands to their river channels (TSC). The effects of TSC on richness, abundance and assemblage structure were examined using PERMANOVA. Assemblage structure in all three invertebrate groups was significantly affected by TSC. Abundance of the two microinvertebrate groups was positively associated by increased TSC. In contrast, abundance of macroinvertebrates and richness in all three groups was unaffected by TSC. Our results support the use of environmental water to increase inundation of these wetlands provide benefits to invertebrates and therefore secondary consumers such as birds.