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The valley floors of semi-arid Australian catchments are generally characterized by floodplain wetland systems with high biodiversity value, however they are threatened by degradation processes brought about by land-use changes. Altered hydrology from large-scale native vegetation clearing and shifting runoff and streamflow regimes have significantly altered floodplain hydrological processes, and often natural resource management decisions within the wider catchment are implemented with limited consideration of lower landscape environments. Our aim has been to develop a spatially distributed ecohydrological model that will allow us to assess the affects of hydrological change and consider optimal management strategies that integrate vegetative and engineering approaches to protect biodiversity assets in the lower landscape. A significant barrier to developing such a tool was addressing the range of spatial and temporal scales that must be considered and the paucity of data available to implement suitable models. To overcome these issues this study adopts a high-resolution model for the floodplain and associated wetlands to simulate in detail the flows, patterns of inundation and riparian hydrology of the valley floor, and this is nested within a coarser scale catchment model able to resolve the essential hydrological dynamics of the surrounding landscape. The model system was applied to the Lake Bryde Natural Diversity Recovery Catchment, located in south-west Western Australia, and model predictions of flow and floodplain inundation were validated against limited data from a flood event that occurred in January 2006. The model system was able to demonstrate the effects of hydraulic constrictions (eg. roads impediments and culvert impacts), likely pre- and post-European behaviours, re-vegetation effects, and altered rainfall patterns on inundation dynamics upon the valley floor conservation areas.