River flows are commonly altered by water resource development, with changes to the natural flow regime potentially impacting riparian vegetation. Increasingly, water resource managers seek to design policy to maintain healthy riparian ecosystems. Models that make explicit the relationship between hydrological variables and vegetation can be used by managers to assess vegetation response under different water management scenarios. We determined the potential impact of water-takeon the spatial distribution of woody riparian plant species in the lower Fitzroy River, in north-western Australia, an area under pressure to increase water resource development. We undertook a plant survey and developed and applied a joint species distribution model to determine the likelihood of occurrence for 26 woody riparian plant species, mapped species occurrence and assessed the change in species distribution under two water-take scenarios. We found that the duration of inundation from flood flows was a strong predictor of species occurrence in our joint species distribution model. We identified species associated with wetter environments, as indicated by their effect size for the inundation metric. Under the 300-Gl water-take scenario we found little change (<2%) in species occurrence, but under the 600-Gl scenario a decline between 5% and 7.4% was predicted for eight species associated with wetter habitats. This decline was generally confined to a localised area. Our approach highlights the usefulness of predictive modelling to identify species most likely to be impacted by water-take, and the benefit of linking modelling to spatial mapping because it can highlight areas where change is likely to occur. This information can assist management to protect ecologically and culturally important species.