The ratio of primary production to ecosystem respiration rates (P:R ratio) is an ostensibly simple calculation that is used to characterize lake function, including trophic status, the incorporation of terrestrial organic carbon into lacustrian food webs, and the direction of carbon dioxide (CO 2 ) flux between a lake and the atmosphere. However, many predictive links between P:R ratios and lake ecosystem function stem from a historically plankton-centric perspective and the common use of the diel oxygen curve approach. We review the evolution of the use of P:R ratios and examine common assumptions underlying their application to (1) eutrophication, (2) carbon flux through lake food webs, and (3) the role of lakes in the global carbon budget. Foundational P:R studies have been complicated principally by the following: most P:R ratios were calculated from mid-lake measurements and failed to incorporate nonplanktonic dynamics; there has been confusion regarding the food web implications when P:R ≠ 1; and CO 2 fluxes between lakes and the atmosphere are influenced by nonmetabolic processes. We argue for a re-assessment, or shoring up, of several fundamental assumptions that continue to guide metabolism research in lakes by accounting for mixing, benthic-littoral processes, groundwater fluxes, and abiotic controls on gas dynamics to better understand lake food webs and accurately integrate lake ecosystems into landscape-scale carbon cycling models.