As recently as a decade ago, a paucity of geographically dispersed and reliable data on mercury (Hg) and methylmercury (MeHg) in water and sediments would have made discussions of large-scale monitoring programs difficult to conceive or implement. Methodological advancements made over this time period, as well as substantial improvements in our overall scientific understanding of mercury sources, cycling and fate in the environment, have enabled scientists, land managers, and regulators to consider how environmental responses to changing mercury emissions and deposition could be monitored. A program whose ultimate goal is to assess environmental responses to changes in atmospheric Hg deposition will undoubtedly rely on sediment and water indicators as critical program components. For both water and sediment, a well established set of sampling protocols and analytical procedures will enable reliable data collection across a diverse set of aquatic ecosystems. Waterbased indicators of Hg and MeHg have already been useful for documenting decadalscale changes in Hg and MeHg concentrations in the Everglades of Florida and a seepage lake in northern Wisconsin. At both sites, changes in Hg deposition were also measured and linked to the environmental response. Unfortunately, there are very few other long-term records of Hg and MeHg in water and/or sediment, thus establishing widespread baselines or current trends is presently difficult. With increasing numbers of studies and monitoring efforts that utilized the collection of water and sediment samples, however, a growing database on Hg and MeHg is evolving that would be useful for site selection and establishing general contamination levels for a more coherent monitoring effort.