Freshwater habitats and wetlands have numerous cultural, recreational and economic values, such as supporting commercial fisheries and as places of ecotourism. Floodplain inundation is an important process in the persistence of these habitats. The alteration of river flows, the loss of flow connectivity, and the degradation or disruption of the physical processes that sustain aquatic food chains threaten both the productivity of these habitats and aquatic biodiversity. It is therefore essential that large-scale assessments of freshwater habitats inform the development of water resource management plans, climate change mitigation and resource monitoring strategies. Yet these assessments are complicated by the inaccessibility of many large wetland systems during times of inundation, making in situ sampling nearly impossible at the time when high levels of aquatic primary productivity are generating food for higher-order aquatic consumers. We used a framework that integrates biophysical indicators (vegetation and inundation) derived from remote sensing with hydrological data (rainfall and river discharge) to undertake a large-scale assessment of the productivity of remote floodplains in the catchments of the Gilbert and Flinders rivers in the southern Gulf of Carpentaria, Queensland.