Based on empirical and synthetic research, lakes make, store, and mineralize organic carbon (OC) at rates that are significant and relevant to regional and global carbon budgets. Although some global-scale studies have examined specific processes such as carbon burial and CO2 exchange with the atmosphere, most studies of lake carbon cycling are from single systems, focus only on a specific habitat, and do not account for all of the major terms in OC budgets. Hence, most lake OC budgets are incomplete, leaving some key processes highly uncertain. To advance the analysis of the role of the inland waters in C-cycling, ecosystem science needs a new generation of studies that confront these shortcomings. Here we address research needs and priorities for improving OC budgets. We present ten key research questions and recommend a framework for essential ecosystem-scale studies of lake OC cycling. Answers to these ten questions will not only improve carbon budgets but also provide robust estimates of lake contributions to global and regional carbon cycling. In addition, studies of lake carbon budgets will provide relative autochthonous and allochthonous carbon fluxes, indicate sources and rates of carbon burial, improve quantification of lake-atmosphere carbon exchanges, better integrate lakes with terrestrial and lotic carbon dynamics, promote understanding of how climate and land-use change will impact lakes, and enable tests of ecological theory related to subsidies and food web stability.