Isotope studies of freshwater aquatic habitats have shown that epiphytic algae in the form of periphyton provides much of the source material for the biomass of secondary aquatic producers. Consequently, methods that can quantify the seasonal abundance of periphyton are important spatial inputs for wetland management and conservation planning processes for tropical floodplains. In this study, estimation of the seasonal spatial variability in floodplain macrophyte and periphyton abundance was made for the floodplains of the Kakadu region in northern Australia. Statistical modelling, using remotely sensed information, was applied to predict the seasonal distributions of macrophyte structural types, which were then combined with the field measurements of periphyton biomass to produce seasonal distributions of floodplain periphyton biomass per unit area. The seasonal spatial distribution of periphyton was strongly influenced by the seasonal variation in macrophyte abundance. Vertical emergent macrophytes (mainly aquatic grasses), covering 70% of the floodplain in May, had the lowest periphyton abundance. Submerged macrophytes, covering 10–15% of the floodplains, had the greatest periphyton abundance. The submerged macrophytes occupied open water areas, mainly in the deeper backswamp areas on the edges of the floodplains, and these areas maintained high periphyton abundance into the dry season. This study provides explicit spatial representation of the seasonal dynamics of tropical floodplain macrophyte and periphyton abundance and presents an approach that can be applied to map ‘hotspots’ of floodplain periphyton abundance.