Conceptual models of lake ecosystem structure and function have generally assumed that energy in pelagic systems is derived from in situ photosynthesis and that its use by higher trophic levels depends on the average properties of individuals in consumer populations. These views are challenged by evidence that allochthonous subsidies of organic carbon greatly influence energy mobilization and transfer and the trophic structure of pelagic food webs, and that size variation within consumer species has major ramifications for lake community dynamics and structure. These discoveries represent conceptual shifts that have yet to be integrated into current views on lake ecosystems. Here, we assess key aspects of energy mobilization and size-structured community dynamics, and show how these processes are intertwined in pelagic food webs.