Flow regimes of river ecosystems worldwide have been modified by humans. Environmental flows aim to sustain the ecological functioning of rivers whilst minimising societal and economic impacts. Evaluating the use of this environmental water is critical to adaptive management and requires specific and quantifiable ecological outcomes. Despite an increasing recognition of the value of managing aquatic systems for ecological processes, evaluation is challenging because we often lack reference-site conditions for functions such as ecosystem metabolism. Here, we used a multi-year dataset from the Lachlan River, a regulated river in Australia’s Murray-Darling Basin, to characterise drivers of ecosystem metabolism and consider approaches to benchmarking gross primary productivity (GPP). Mean annual rates were high compared to rivers globally, with daily rates peaking in summer under high light conditions. Flow variability tended to reduce daily GPP, especially during warm periods, perhaps due to the physical disturbance of established biofilms. This negative effect of flow on GPP was also observed specifically during freshes delivered with environmental water, suggesting that these actions contributed to the avoidance of high algal biomass. Compared to international literature-derived criteria, environmental water delivery improved the river condition from ‘satisfactory’ to ‘good’, demonstrating that regulated rivers can be successfully managed for ecosystem processes. However, the relevance of these specific criteria to rivers in the Murray-Darling Basin remains unclear. We explore whether these targets could also be informed by considering the primary productivity required to support key primary consumers, zooplankton and shrimp. Linking management outcomes based on ecosystem processes to water quality and food-web responses will provide a more holistic picture of ecosystem health, ensuring optimal use of environmental water.