River floodplains and riparian zones are disproportionately important habitats for vertebrate fauna worldwide, and are prominent in fragmented landscapes. Landscape-scale changes in both hydrology and vegetation in these systems have implications for habitat condition and organism movements, and consequently for biodiversity persistence. However, water resources and the terrestrial landscape are usually managed separately, often by different management bodies. Consequently, river floodplains and riparian zones are rarely incorporated into landscape-scale conservation in a truly integrated way. Yet the dual mediums of water and vegetation interact to create complexities and interdependencies that are unique to these systems, especially over time. Improving understanding of the relative influence of hydrological and vegetative connectivity on semi-aquatic and terrestrial fauna species could reveal better ways to combine water and land management and implement more integrated landscape-scale conservation approaches. Here we present a series of conceptual models developed to synthesise current understanding of how key processes influence the persistence of terrestrial and semi-aquatic vertebrates in river floodplains and riparian zones. We define three major functional groups of species based on their relative dependence on water and associated vegetation for habitat or movement, and describe conceptual models for each functional group built from the ground up, synthesising models for multiple Australian species in each group. We translate these models into spatially and temporally explicit management goals to explore useful synergies and generalisations across functional groups, and ways in which landscape management can integrate spatial and temporal variability in vegetation and water to support a full suite of species.