Water resource development in south-eastern Australia has resulted in serious reductions in the frequency with which floodplain woodlands are inundated, resulting in significant habitat degradation. Forecast changes in management practices and climate are likely to result in further changes to flood regimes for floodplain woodland remnants; however the potential effects of such changes are poorly understood. This study demonstrates that differences in flood frequency are associated with predictable shifts in site character and ultimately transitions to different vegetation and fauna communities, even within the same broad vegetation type (Eucalyptus largiflorens black box woodlands). These shifts have a synergistic effect resulting from interactions between vegetation changes, fauna habitat preferences and fauna behaviour. Such transitions encompass changes in structure and composition of a community or site; with potentially far-reaching implications for ecosystem function and biodiversity persistence at multiple scales and for the way a site is valued and managed. Knowledge of the nature of these shifts allows land and water managers to make informed decisions about site management according to what they regard as desirable characteristics. Desirable characteristics may be relevant to broad scale management, such as entire landscapes, or to fine scale targeted management, such as management of threatened or invasive species.