Globally, river regulation and water extraction for anthropogenic use have altered the hydrology and ecology of riverine and floodplain ecosystems. Managed environmental flows are increasingly being implemented to restore the condition of many riverine and floodplain ecosystems. In the Murray-Darling River Basin, south-eastern Australia, appropriate flooding regimes are key to maintaining populations of the dominant floodplain forests and woodland trees, River Red Gum (Eucalyptus camaldulensis) and Black Box (E. largiflorens). We investigated the effects of three environmental flow events and microsite attributes (bare ground, canopy and understorey vegetation) on eucalypt recruitment over a five-year period across a semi-arid floodplain gradient (lake bed, lower and higher floodplain). Eucalypt recruitment increased after the environmental flows. The probability of recruitment declined with increasing elevation along the floodplain gradient, with the highest occurrence on the lake bed and lower floodplain where River Red Gum dominates. Recruitment on the higher floodplain, where Black Box is dominant, was low, suggesting that factors other than flooding (e.g. poor tree health) may limit regeneration. Recruitment also increased with increasing cover of bare ground and understorey vegetation. Saplings (>1 m) were more likely to occur on the lower floodplain, where understorey vegetation cover approached 50 %, suggesting that the germination and survival niches of eucalypts may differ. That is, bare ground is necessary for germination, while understorey vegetation may provide protection to seedlings from desiccation and browsing. The combined flood events likely benefited the survival of pre-established seedlings by limiting the effects of summer desiccation and increasing soil moisture availability. There may be a trade-off between managing environmental flows for seed germination versus seedling survival. Future environmental flows that target the higher floodplain are likely to contribute to improvements in tree health, reproductive output and subsequent recruitment opportunities in this floodplain ecosystem. This study shows that environmental flows likely contribute to the maintenance of sustainable eucalypt floodplain forests and woodlands through the facilitation of recruitment and seedling persistence.