Methane is a powerful greenhouse gas, and atmospheric concentrations have risen 2.5 times since the beginning of the Industrial age. While much of this increase is attributed to anthropogenic sources, natural sources, which contribute between 35% and 50% of global methane emissions, are thought to have a role in the atmospheric methane increase, in part due to human influences. Methane emissions from many natural sources are sensitive to climate, and positive feedbacks from climate change and cultural eutrophication may promote increased emissions to the atmosphere. These natural sources include aquatic environments such as wetlands, freshwater lakes, streams and rivers, and estuarine, coastal, and marine systems. Furthermore, there are significant marine sediment stores of methane in the form of clathrates that are vulnerable to mobilization and release to the atmosphere from climate feedbacks, and subsurface thermogenic gas which in exceptional cases may be released following accidents and disasters (North Sea blowout and Deepwater Horizon Spill respectively). Understanding of natural sources, key processes, and controls on emission is continually evolving as new measurement and modeling capabilities develop, and different sources and processes are revealed. This special issue of Limnology and Oceanography gathers together diverse studies on methane production, consumption, and emissions from freshwater, estuarine, and marine systems, and provides a broad view of the current science on methane dynamics of aquatic ecosystems. Here, we provide a general overview of aquatic methane sources, their contribution to the global methane budget, and key uncertainties. We then briefly summarize the contributions to and highlights of this special issue.