Understanding the key ecological factors that moderate the relationship between biodiversity and the productivity of ecosystems is a major challenge for ecological research. Here we show that the relationship between the species richness of primary producers and net rates of biomass production in streams depends on the history of discharge-related disturbances. Using common methods to study 83 streams in the mid-Atlantic United States, we demonstrate that a positive relationship between producer richness and the net production of biomass only occurs in streams characterized by highly variable, unpredictable discharge regimes that represent frequently disturbed environments to benthic organisms. This pattern is partly explained by predictable changes in the composition of species assemblages among disturbed streams. The pattern also results because, in disturbed systems, species have faster rates of biomass accumulation when they are a part of species-rich assemblages. We discuss several possible explanations for this result. Our study supports qualitative predictions from theoretical and small-scale experimental work that the strength of the diversity-productivity relationship will depend explicitly on the disturbance regime of an ecosystem. The results have important implications for the management and conservation of aquatic resources as they suggest that changes to the productivity and diversity of streams may have their greatest impacts on organisms and systems that are most sensitive to disturbance.