In Australia’s hydrologically unpredictable inland rivers, casual factors driving recruitment of native fish remain poorly understood. Since European settlement, native fish populations have declined while introduced, non-native fish have flourished, favoured by river regulation. Attempts to restore native fish populations have centered on targeting environmental flows to promote native species while suppressing non-native species; however, the benefits of such restoration efforts are unclear. This study investigated the native and non-native fish community within the heavily regulated, semi-arid floodplain system of the Macquarie Marshes, NSW. I measured the response of fish communities to a large one-in-10yr flood event, sustained by targeted environmental flows. Ephemeral floodplain sites were regularly sampled for larval, juvenile and small-bodied fish over a six-month period and the micro-habitat use and community structure of both native and non-native species recorded. A total of 20,737 individual fish, representing eight species in seven families, were captured. Native fish recruits were largely absent and non-native species dominated fish communities across every stage of the flood, outnumbering native fish 16:1. Micro-habitat overlaps between natives and non-natives also occurred at all stages indicating high resource competition pressures. We also captured the first known record of the native Hyrtl’s tandan, Neosilurus hyrtlii, in the Macquarie river catchment, highlighting the potential restoration benefits large-scale floods can provide via hydraulic connectivity.