The frequency and intensity of flood and drought events is expected to intensify with global warming, effecting estuarine ecosystems. Yet the response to climatic events also depends on the environmental conditions in between events. A long-term monitoring data set on macroinvertebrates from the estuary of the Murray River allowed to compare the effects of two flood events and the subsequent recovery. One flood event (2010/11) occurred after the Millennium Drought, and the second flood event (2022/23) after the high rainfall of consecutive La Niña years. Both flood events caused a decrease in macroinvertebrate abundances in the estuary. Recolonisation of the estuarine mudflats by macroinvertebrates took several years after the drought-breaking 2010/11 flood, whereas recolonisation commenced within a year following the 2022/23 flood. The increased resilience of macroinvertebrates to the recent flood event was facilitated by a decade of continuous flows and a few years of elevated flow volumes which had enabled an extension of the estuarine community into the previously hypersaline Coorong lagoon. The establishment of an estuarine macroinvertebrate community in the lagoon provided source populations for the recovery of the estuary. Understanding such mechanisms for resilience can inform future management of environmental flow.