Advances in measuring open-system metabolism suggest that most streams and many lakes are net heterotrophic, and therefore allochthonous carbon may be a universal driver of ecosystem metabolism.  Yet, studies of diets and carbon assimilation demonstrate that high quality algal carbon may fuel a larger proportion of production by primary consumers than would be predicted given its availability.  Likewise, terrestrial invertebrates are a small flux to freshwater habitats, but a high quality prey source that have been shown to contribute disproportionately to fish production.   However, ecosystem metabolism measures are insensitive to the importance of such energetic pathways involving higher consumers, and therefore inadequately describe the importance of allochthonous and autochthonous carbon for aquatic food webs.  We hypothesize that the relative contributions of carbon sources to food webs, and the net trophic state of freshwater ecosystems, is mediated by consumer selection for high quality food.  We review the literature regarding autotrophy vs. heterotrophy, and allochthony vs. autochthony, and describe a framework for integrating carbon source vs. utilization information that helps redefine our understanding of the trophic state of freshwater ecosystems.  This analysis has important implications for understanding the food base of aquatic consumers, and how anthropogenic change modifies energy flow in freshwaters.