The ecosystem of a tide-affected estuary consists of an extremely complicated balance of natural processes and human induced activities. Some of the basic characteristics of such a system, for example the San Francisco Bay estuarine system, are not well understood. A comprehensive description of the hydrodynamics and the related transport phenomena is still lacking. A better understanding of the effects among the interactive natural and human induced processes on this system requires advances in basic science relating the physical, chemical and biological estuarine processes. Circulation in a tidal estuary is generated in response to astronomical tides, inflow of fresh water, winds, and stratification due to salinity. The basin topography (bathymetry), air-water interaction, water sedimentation interface, mixing characteristics, frictional loss at the bottom, and the rotational effects of the earth, together with the above mentioned driving forces, constitute an extremely complicated balance that conserves mass, momentum, energy, and conservative solutes in the system. Objectives are to understand processes and rates by which water, salt, and other solutes interact; develop methods to enable quantification of the relative importance of river inflow, winds, tides and other dynamic forcings that act upon the system; and develop and verify conceptual and numerical models of these interactions. For current information about work being done by this project, see project's home page.