The flow regime of rivers worldwide has been impacted by the storage and extraction of water for consumptive uses. In Australia’s Murray Darling Basin, flow regulation has resulted in reduced flow magnitude, lower flow variability and seasonal flow reversal, with consequences for the way that organic carbon is generated and incorporated in aquatic food webs. Long-term monitoring suggests that high light availability and temperatures combined with low and steady flows generally increase rates of gross primary productivity by plants and algae. However, these relationships are inconsistent among sites and may not capture contributions by littoral and fringing wetlands to ecosystem-scale productivity. To address this, we used a hydraulic rating method to develop a relationship between potential gross primary productivity and discharge. This enabled us to explore mechanisms and identify breakpoints, defined as a threshold flow where a change in depth may rapidly influence whole-river productivity. The model is based on measurements of algal biomass combined with channel geomorphology and light attenuation from the Lachlan River, central NSW. Our results show that primary productivity responses to changes in flow depend on 1) the initial flow magnitude, 2) channel geomorphology, and 3) the balance of water-column versus benthic productivity. This model demonstrates why idiosyncratic responses may be observed among different sites at different times. We envision this model could inform water managers on the most effective use of environmental water resources to maintain primary productivity within a satisfactory range.