Developing a common understanding of how key biotic components of the ecosystem respond to management interventions is a critical element for improving conservation outcomes. The dynamic nature of floodplain ecosystems and underlying spatial heterogeneity present a range of challenges. We developed multi-taxa approach which summarised the inter-annual dynamics across two large floodplain wetland systems. First, we developed spatially explicit models linking river and wetland hydrological data to floodplain inundation able to quantify the spatial variability in model fit across the floodplain. When developed response models between a suit of ecological indicators derived from long-term monitoring data including vegetation, fish, frogs and waterbirds with wetland and floodplain hydrology using Generalized Mixed Effect Models. We found that rather having common responses at the floodplain scale, responses of ecological indicators were spatially variable and nested within different eco-hydrological units. There were also significant differences between taxa and functional group responses to inundation and subsequent predicted response to water management interventions. As the available ecological response data were largely derived from years with either small flows events (<40% floodplain inundated) or the occasional large flow events (>75% floodplain inundated), it was difficult to estimate potential outcomes for moderate (40 -75% floodplain inundation), once been a common feature of these floodplains. Findings allowed us to set area-specific management targets for inundation that were able to achieve best ecological outcomes. Combining developed ecological response relationships and water availability scenarios using Bayesian Belief Networks also provided an intuitive framework for managers to compare potential ecological outcomes under different water management scenarios.