Stream metabolism provides a measure of whole ecosystem response to changes in hydrologic or other conditions. Floods and flows can influence river food webs by adding organic matter to the river, altering the energy sources available for primary production. Changes in dissolved oxygen reflect the sources and utilisation of organic carbon. Dissolved oxygen loggers were used to continuously monitor for extended time periods over the course of seven years from 2015 to 2022 in the Warrego River and in the Darling River. Daily dissolved oxygen was used in combination with important physical, chemical, and biological variables to explain variation in gross primary productivity (GPP) and ecosystem respiration (ER) under different hydrological conditions. Metabolic fingerprints were used to visualise spatial and temporal changes in ecosystem metabolism by producing “fingerprints” for each study site under different flow conditions. Net ecosystem production in both the Warrego and Darling Rivers tended towards heterotrophy, but varied daily in response to changes in flow and the addition of environmental water to the system. Increased data quality and the inclusion of periods of high flow and water levels in ongoing monitoring will improve our understanding of the relationship between flow and productivity in these rivers.