“Trophic state” is often used to classify aquatic ecosystems according to biotic productivity. Primary productivity (or a surrogate for it) has always been used as the metric of trophic state. We make the case here that both primary production and key heterotrophic processes are needed to evaluate trophic state. Defined as the relative flux rate of carbon (C) into the food web, trophic state is a fundamental property that is intimately related to both ecosystem structure and how humans influence water quality. Rates of heterotrophic activity can exceed primary production in many aquatic ecosystems including oceans, lakes, and streams. A comprehensive definition of trophic state with respect to aquatic food webs requires accounting for both the oxidation of organic C (respiration) and photosynthetic fixation of inorganic C (primary production). This inclusive definition is required because food webs can be fueled in part by allochthonous C. We propose autotrophic and heterotrophic states be defined by rates of photosynthetic and respiratory C fluxes respectively, and both be used to characterize ecosystems. Cumulative frequency distributions of both can be developed for minimally impacted aquatic systems as a baseline against which to compare human-influenced sites as well as for describing the range of conditions that aquatic organisms have experienced in their recent evolutionary history. Subsidies of organic C and inorganic nutrients to aquatic ecosystems influence heterotrophic state, so characterizing the base of the food web necessitates a stoichiometric view of supply rates, use efficiencies, and recycling of inorganic and organic materials.