Policies designed to address current challenges to the sustainability of fisheries generally use an ecosystem‐based approach – one that incorporates interactions between fishes, fishers, and the environment. Fishing alters the trophic structure among coral reef fish but properly assessing those impacts requires an understanding of how and why that structure varies naturally across scales. Using a combination of small‐ and large‐scale surveys, we generated biomass pyramids for 20 uninhabited Pacific islands, and found that (1) the distribution of reef fish biomass across trophic levels is highly scale dependent: trophic structures that appear top‐heavy at small scales can take a variety of different states when data are integrated across the broader seascape; (2) reefs can have the greatest biomass at intermediate consumer levels, which we describe as “middle‐driven” systems; and (3) in unfished coral reef systems, trophic structure is strongly predicted by energy into the base and middle of the food web, as well as by the interacting effect of water temperature.