Measurements of the production and consumption of organic material have been a focus of aquatic science for more than 80 years. Over the last century, a variety of approaches have been developed and employed for measuring rates of gross primary production (Pg), respiration (R), and net ecosystem production (Pn = Pg ? R) within aquatic ecosystems. Here, we reconsider the range of approaches and applications for ecosystem metabolism measurements, and suggest ways by which such studies can continue to contribute to aquatic ecology. This paper reviews past and contemporary studies of aquatic ecosystem-level metabolism to identify their role in understanding and managing aquatic systems. We identify four broad research objectives that have motivated ecosystem metabolism studies: (1) quantifying magnitude and variability of metabolic rates for cross-system comparison, (2) estimating organic matter transfer between adjacent systems or subsystems, (3) measuring ecosystem-scale responses to perturbation, both natural and anthropogenic, and (4) quantifying and calibrating models of biogeochemical processes and trophic networks. The magnitudes of whole-system gross primary production, respiration and net ecosystem production rates vary among aquatic environments and are partly constrained by the chosen methodology. We argue that measurements of ecosystem metabolism should be a vital component of routine monitoring at larger scales in the aquatic environment using existing flexible, precise, and durable sensor technologies. Current and future aquatic ecosystem studies will benefit from application of new methods for metabolism measurements, which facilitate integration of process measurements and calibration of models for addressing fundamental questions involving ecosystem-scale processes.