Harvesting threatens many vertebrate species, yet few whole-system manipulations have been conducted to predict the consequences of vertebrate losses on ecosystem function. Here, we show that a harvested migratory detrital-feeding fish (Prochilodontidae: Prochilodus mariae) modulates carbon flow and ecosystem metabolism. Natural declines in and experimental removal of Prochilodus decreased downstream transport of organic carbon and increased primary production and respiration. Thus, besides its economic value, Prochilodus is a critical ecological component of South American rivers. Lack of functional redundancy for this species highlights the importance of individual species and, contrary to theory, suggests that losing one species from lower trophic levels can affect ecosystem functioning even in species-rich ecosystems.