Context Riverine systems consist of distinct habitats along a landscape gradient and characterising the composition and structure of vegetation in these habitats can support environmental water-management decisions. However, in many regions, including northern Australia, there is a paucity of hydro-ecological data. Aims We aimed to characterise the species composition and the structure of riparian and floodplain woody vegetation of the lower Fitzroy River. Methods We surveyed woody vegetation in different habitats within the riparian zone and floodplain. Multivariate analysis was used to assess differences in the composition of riparian woody species among the four habitat types and univariate analysis was used to compare vegetation structure, recruitment, and environmental variables among habitats. Key results The composition and the physical structure of woody species differed among habitat types of the lower Fitzroy River, indicating a zonation of riparian and floodplain vegetation in response to fluvial processes and water availability. The floodplain was characterised by sparsely distributed Eucalyptus microtheca and a sparse (∼30%) canopy cover. In contrast, the riverbank habitat type had very large trees (mean basal area = 0.26 m2), with a dense canopy cover (∼80%) and was dominated by Melaleuca argentea, M. leucadendra and Barringtonia acutangula. Both the top of bank and off-channel wetlands represent a more intermediary environment, characterised by greater species richness and greater seedling recruitment. Conclusions Identifying these habitat types and characterising their physical and biological properties, such as the relationship between flooding and the composition of woody species, provides a framework to assist the management of large floodplain river systems.