This chapter reviews research on ecosystem metabolism in coastal environments, focusing on the history of methods development, spatial/temporal variations in rates, controlling factors, and application of these methods to address diverse scientific questions. Essential concepts and widely used terms are defined and explained. The wide range of ecosystem metabolism methods are organized conceptually, and each approach is described with the discussion of important strengths and limitations. Published scientific literature and public-access data are used to review the collective knowledge regarding physical (light, temperature, depth, and flushing) and chemical (inputs of nutrients and organic matter) factors that regulate the ecosystem rates of apparent daytime production (Pa), nighttime (or dark) respiration (Rn), gross production (Pg), and net ecosystem production (Pn). Given these controlling factors, we describe spatial and temporal patterns and gradients in ecosystem metabolism that have been reported for different estuaries and coastal systems, including seasonal, daily, and annual scale cycles as well as metabolic trends across the land–sea gradient. We discuss a range of representative examples of how ecosystem metabolism measurements have been applied to address important research questions. These applications include comparative analysis of trophic status in terms of magnitude and balance of metabolic rates and studies of relationships between metabolic balance (e.g., Pn or Pa/Rn) and physical transport of organic carbon and inorganic nutrients. Also included are studies that quantify the relative contributions of specific biomes, habitats, or regions to large-scale integrated rates of ecosystem metabolism. Further review illustrates how these rates have been used to understand controls and relative contributions of physical and biological processes to O2 depletion and coastal hypoxia. This chapter also focuses on the inherent linkage between ecosystem metabolism and quantitative analysis of coastal food webs, where Pa, Rn, and Pn measurements provide robust constraints on trophic flux network models and facilitate a deeper understanding of the relationships between trophic structure and integrated metabolic rates. This chapter also illustrates how ecosystem metabolism responds to a spectrum of anthropogenic perturbations, including inputs of nutrients, labile organics, and toxic contaminants, as well as field observations relating Pn to climate-linked watershed runoff and shifts in coastal circulation. The final synthesis describes broad patterns of metabolic balance in coastal ecosystems as well as how these change in response to external perturbations including climate change. Priority topics for future research directions are identified, including new methods to quantify measurement errors and computation errors that would facilitate rigorous extrapolation from individual observations to larger scales as well as the partitioning of large-scale calculations into contributions from biotic subsystem components.