Recent modeling developments are supporting large-scale examinations of the patterns and controls on riverine gross primary production (GPP), including links to river regulation and dam management. In the Colorado River downstream of Glen Canyon Dam through Grand Canyon, Arizona, USA, GPP is considered a proxy for aquatic food availability to consumers in this ecosystem, where 1) the food web is largely autochthonous (derived in situ by algal photosynthesis) and 2) large standing stocks of less-palatable primary producers are lacking. Here we present 12 years of GPP estimates from three long-term monitoring sites in the Colorado River through Grand Canyon. We model drivers of GPP in this frequently turbid river that undergoes extreme change in water quality drivers. We describe the impact of experimental high flows on rates of GPP and show that effects vary based on the seasonal timing of the flows. We also find a lack of synchrony between sites, with temperature more strongly correlated with GPP in the reach furthest downstream, and turbidity more strongly correlated with GPP in the reach nearer the dam. In the Colorado River, a river discontinuum created by large-scale dams contributes to the temporal decoupling of disturbances, specifically turbidity, disturbance flows, phosphorus, and temperature.