Stable water levels and turbidity associated with flow regulation in the River Murray have promoted the growth of filamentous green algae and Cyanobacteria in biofilms on submerged wood. We investigated the assimilation of biofilm algae by two dominant consumers, the decapod crustaceans Macrobrachium australiense (Palaemonidae) and Paratya australiensis (Atyidae), in two river reaches differing in the extent of floodplain development, hence wetland connectivity. Filamentous Cyanobacteria, a major part of the biofilms assimilated in combination with other foods, were up to 83% of the algal component of the gut content volume of P. australiensis and 44% that of M. australiense. Cyanobacteria have not previously been reported as a major source of nutrition for adult decapods. There was little difference between the stable isotopic signatures (13C/12C, 15N/14N) of the two decapod species, or between decapods in the two reaches. Coarse and fine particulate organic matter from the gorge had similar isotopic signatures to those from upstream and so were likely derived from macrophyte detritus rather than local willows. Red gum leaves and wood were too depleted in both δ13C and δ15N to register in the diets of either decapod in gorge or floodplain reaches. The most likely food sources for the decapods are littoral plants in the gorge reach and fine particulate organic matter material processed upstream. This is consistent with current hypotheses of organic matter flux in large river systems.