ECCO was established in 1998 as part of the World Ocean Circulation Experiment (WOCE) with the goal of combining a general circulation model (GCM) with diverse observations in order to produce a quantitative depiction of the time-evolving global ocean state. The importance of such an endeavor is recognized by numerous national and international organizations, such as the WMO's World Climate Research Programme (WCRP) and UNESCO's Intergovernmental Oceanographic Comission (IOC). These programs have all noted the necessity of synthesizing the diverse remotely-sensed and in-situ observations with known dynamics and thermodynamics through a GCM. ECCO products are in support of the Climate Variability and Predictability (CLIVAR) programme and the Global Ocean Data Assimilation Experiment (GODAE).

ECCO was initially formed under the National Ocean Partnership Program (NOPP) with funding provided by the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), the Office of Naval Research (ONR), and now the National Oceanic and Atmospheric Administration (NOAA). Its long term goal is to provide a high resolution coupled ocean/sea-ice/biochemical (and ultimately, consistent atmospheric) state estimate to a wide community. In contrast to so-called numerical weather prediction, these estimates will include the ocean's history as well as predictions. ECCO's efforts toward this goal now include several projects, each of which is bringing ECCO closer to its long term goal, while providing significant scientific contributions.