AbstractFlow regulation of montane and alpine headwater streams can fundamentally alter food web structure and energy flows through changes in productivity, resource availability, and community assembly. Dam flow‐release schemes can be used to mitigate the environmental impacts of flow regulation via environmental flows, which can increase discharge variability and other ecologically important hydrological properties. In particular, managed floods can reintroduce disturbance to the system and stimulate the reactivation of physical habitat dynamics. However, how managed floods might restore ecosystem processes is virtually unknown. In this study, we examined patterns in potential energy fluxes before, during and after a long‐term experimental flood program on the river Spöl, a regulated alpine River in southeast Switzerland. We used benthic samples collected during long‐term monitoring and stable isotope analysis (δ¹³C and δ¹⁵N) of macroinvertebrates and their potential food sources to reconstruct secondary production, and potential energy fluxes, over a 20‐year study period. The experimental floods did not alter the relative importance of basal resources but resulted in a considerable decline in secondary production, which remained low after the discontinuation of the floods. Our data suggest that a lack of recolonization by mosses following the discontinuation of the experimental flood program on the river Spöl may have driven patterns in energy fluxes by limiting macroinvertebrates using mosses for habitat. The effects of environmental flows on energy flows in this system thus depend on flood disturbance and the environmental context following the discontinuation of floods.