Lowland riverine–floodplain systems often have significant but irregular inputs of allochthonous carbon. However, the importance of this carbon to riverine systems remains poorly understood. We assessed open water dissolved organic carbon (DOC) concentrations, metabolism and biofilm stable isotope (δ13C) signatures, upstream and downstream of an extensive floodplain forest on the Murray River, Australia, before and after a flood event. Prior to flooding, all sites had similar concentrations of DOC, rates of metabolism and biofilm δ13C signatures. During the flood DOC concentration increased up to three-fold downstream of the forest, gross primary production (GPP) increased at all sites, but community respiration (CR) increased only at the downstream sites, resulting in decreased in NPP downstream and a slight increase upstream. Biofilm δ13C signatures became depleted by between 4 and 7‰ downstream of the forest during the flood, reflecting a rapid incorporation of allochthonous carbon into the biofilm. These results indicate that flooding led to a substantial increase to the energy budget of the Murray River through the provisioning of large quantities of allochthonous carbon and that terrestrial carbon was processed within the river biofilms. Allochthonous carbon assimilation within biofilms during flooding provides a potential pathway for allochthonous carbon to be incorporated into the metazoan foodweb.