Free-flowing tropical rivers are some of the most dynamic ecosystems in the world and they support a diverse range of fisheries and trophic guilds from herbivores and detritivores to top predators. Tropical Australian rivers are characterized by annual wet-dry cycles. The wet season is driven by monsoonal rains which come in summer, followed but low to no rainfall throughout the dry season. During the dry season, perennial wetlands provide refuge habitat and often get isolated from the main river channel. Here, we explore how dry season food quality and fish community trophic structure vary among wetland and river channel environments. Bulk stable isotope and fatty acids of primary producers and fish tissues were analysed from up to 30 individuals of four trophic groups sampled in river-floodplain environments of the free-flowing Roper River in northern Australia. Differences in fatty acid profiles of fish trophic groups (primary consumers, omnivores, invertivores and predators) were observed and varied between clear oligotrophic and turbid meso-trophic wetlands, and between river channel and wetland environments. Low and high trophic level consumers of free-flowing rivers appear to gain essential fatty acids from diverse range primary produces across river-floodplain environments. Our results suggest that anthropogenic pressures which increase sediment loads and turbidity in wetlands may result in bottom-up food quality trophic cascades, and that maintaining lateral connectivity between river channel and floodplain wetlands should be a priority for tropical river conservation and management.