The connection of rivers to their floodplains is known to facilitate a significant food subsidy to aquatic consumers - the flood pulse advantage. Although rivers in northern Australia are largely unimpacted by water resource development, there is considerable natural variation in the pattern of hydrological connectivity with their floodplains - in both space and time. This has been shown to influence the strength of subsidies to river food webs. Large mobile consumers in particular show a high level of dependence on subsidies from outside of the river channels they inhabit for much of the time. Our recent work, using conservative isotope tracers, in the Alligator Rivers Region suggests that mobile consumers derive much of their somatic growth from feeding in specific locations within inundated floodplains. These tend to be deeper areas that retain open water with submerged macrophytes throughout the wet season. Submerged macrophytes support a high level of epiphytic algae production, an important basal food resource for aquatic consumers, compared with other structural types. Changes to flow regimes that diminish the depth or duration of inundation of these 'hotspots' of high quality food resources, or the presence of barriers that restrict access of mobile consumers to them, are likely to have a significant impact on this important subsidy to river food webs and fisheries.