Floodplain wetlands play a significant role in the storage of sediment and water and support high levels of nutrient cycling that is driven by intermittent inundation. In regulated rivers, there is often a reduction in the frequency and duration of inundation and managed floodplain inundation is used as a tool to help restore wetlands. It is important to quantify the outcomes of re-introducing water to floodplain wetland systems. We examined the effects of environmental floodplain watering on water quality and three groups of invertebrates, including benthic and pelagic microinvertebrates and macroinvertebrates, in two wetlands systems on the Gwydir River system in the north of the Murray-Darling Basin. We hypothesised that a wetland inundated for longer periods of time would have altered water quality and support a greater richness and abundance of invertebrates, thus altering their assemblage structures. Water quality and the assemblage structure of all three invertebrate groups in the wetlands was significantly influenced by the time since connection (TSC) to their rivers and therefore the length of inundation. However, the response of water quality and the microinvertebrate assemblages to TSC differed between the two wetlands. Water quality was affected by an increase in six variables, including the nutrient TN and a decrease in the nutrient SRP. Microinvertebrate abundance was positively associated with TSC, but the abundance of macroinvertebrates was not. The relationships demonstrated between TSC and invertebrates indicate that the duration of inundation is important in maintaining the ecology and food webs in these and other semi-arid floodplain wetlands.