This dataset contains best estimates and uncertainties for mean annual fluxes of inorganic, organic, and total (organic + inorganic) carbon in tidal wetlands, estuaries and shelf waters of eastern North America, which is defined by the coastline running between the tip of the Scotian Peninsula (Canada) and the southern tip of Florida (USA). The data are provided on a per-unit-area basis and as spatially integrated values for each of the three ecosystem types (tidal wetlands, estuaries, and shelf waters) and the entire coastal ecosystem (tidal wetlands + estuaries + shelf waters) as well as for three geographic subregions (the Gulf of Maine, the Mid-Atlantic Bight, and the South Atlantic Bight) and the entire Eastern North America domain (Gulf of Maine + Mid-Atlantic Bight + South Atlantic Bight). The data include the net uptake from the atmosphere by the three ecosystems; burial in tidal wetland soils, estuarine sediments, and continental shelf sediments; riverine input from land to estuaries; and the net lateral advective transports from ecosystem to ecosystem. In addition, heterotrophic respiration (HR), net primary production (NPP), and net ecosystem production (NEP) estimates were computed for each ecosystem. The fluxes were derived using a variety of sources and are estimates for average conditions over the past decades from data covering roughly the period 1976-01-01 to 2017-12-31.