Disturbance is a strong driver of forest ecosystem species composition. Understanding how current management interacts with disturbance is critical for implementing effective strategies to promote native species. Our manipulative BACI experiment evaluated whether ecological thinning promoted a diverse native understorey in an extensive semi-arid floodplain forest that has experienced widespread woody thickening from historical logging and regulated river flows. We monitored three measures of vegetation (native plant richness; ratio of native to introduced richness; species occupancy) for one year prior to, and five years following ecological thinning, encompassing two flood disturbance events. We asked: Does vegetation response to recent flooding and thinning disturbance depend upon legacy tree densities and site productivity? Under which conditions does thinning promote native understorey species? Strong three- and four-way interactions (initial tree density, productivity, recent river flow, thinning intensity) for both measures of richness highlighted that the few positive effects of thinning were spatially and temporally variable. Native richness peaked during low to average river flow in high productivity sites with low initial tree densities and low thinning intensity (<15 %). Often, increases in native richness due to thinning were accompanied by even greater increases in introduced richness. Species occupancy responded to site productivity, floods and tree densities that existed prior to thinning, irrespective of thinning intensity. Together, this demonstrates that in short timeframes ecological thinning alone will not restore understorey composition altered by woody thickening. Promoting diverse pathways of recovery from legacy and current disturbances requires greater understanding of how legacy effects persist.