Environmental flow releases in lowland Australian rivers are currently timed to avoid high-carbon production on floodplains. Moreover, return flows (water draining from floodplains back into rivers) are avoided if there exists a risk of introducing deoxygenated “blackwater” into the main channel. This concern has restricted the range of possible watering scenarios being considered by environmental flow managers. We utilised a series of blackwater flows in the lower Murrumbidgee floodplain, Australia, in 2016 and 2017 to determine the origin and trophic contribution of blackwater dissolved organic carbon (DOC) in a floodplain wetland. We demonstrate a consistent difference in the isotope signature of blackwater DOC compared to both dissolved inorganic carbon (DIC) and river water DOC, explained by the greater contribution of floodplain vegetation (including the river red gum Eucalyptus camaldulensis) to blackwater DOC. Stable carbon isotope signatures suggest a contribution of blackwater to algal production, whereby microbial-mediated conversion of blackwater DOC into DIC may create opportunities for primary autotrophic productivity. This carbon signature was incorporated by the common yabby Cherax destructor. In the main river channel, C. destructor, the native gudgeon Hypseleotris spp. and the introduced European carp Cyprinus carpio may utilise the same basal carbon source. The use of small to moderate floodplain inundation with return flow to the river, properly monitored, would ameliorate the risk of hypoxia while providing the benefit of floodplain-derived DOC and associated increases to in-stream productivity.