Size is a fundamental organismal trait and an important driver of ecosystem functions. Although large individuals may dominate some functions and provide important habitat structuring effects, intra-specific body size effects are rarely investigated in the context of BEF relationships. We used an in situ density manipulation experiment to explore the contribution of large, deep-burrowing bivalves to oxygen and nutrient fluxes across the sediment-water interface. By manipulating bivalve size structure through the removal of large individuals, we held species identity constant, but altered the trait characteristics of the community. The number of large bivalves was the best predictor of ecosystem functioning. Our results highlight that (a) accounting for body size provides important insights into the mechanisms underpinning biodiversity effects on ecosystem function, and (b) if local disturbances are recurrent, preventing individuals from reaching large sizes, the contribution of large adults may be lost, with largely unknown implications for ecosystem functionality.