Understanding the origin of carbon in floodplain river systems is integral to ecosystem health, and overall biotic growth. It is also a contentiously argued topic with various hypotheses (river continuum concept, ﬂood-pulse concept, and riverine productivity model) that assign the sources of carbon as either allochthonous or autochthonous. Despite the significance of this issue for ecological understanding and adaptive management of environmental water, there is little knowledge of the sources of carbon that underpin larval fish food webs in Australian floodplain rivers. It is known that fish recruitment is strongly influenced by the availability of suitable food resources, particularly microinvertebrates that provide critical prey for larval fish of all species. Due to this strong link between larval fish and microinvertebrates, a limited supply of microinvertebrates can be a key factor causing failed recruitment and high initial mortality of larval fish. In a food-web based approach, focusing on larval fish and their prey, stable isotope analysis (SIA) will be performed to investigate relationships between and within biota, their diet and surrounding environment. The nutritional value of a range of microinvertebrate taxa will also be examined. The food webs of larval fish in regulated and unregulated catchments will be compared to investigate the impact of water abstraction and dams on sources of carbon. Knowledge from this research will support adaptive management of fish recruitment in regulated rivers.