Modeling salt intrusion in the San Francisco Estuary prior to anthropogenic influence

Anthropogenic changes have dramatically transformed the upper San Francisco Estuary over the past two centuries. Key changes influencing the region's hydrology and hydrodynamics include land use changes, levee construction and channel modifications, upstream reservoir construction, and out-of-basin water exports. In order to examine how these changes have altered the physical characteristics of the estuary, 3-D hydrodynamic models were constructed to study the system in its "pre-development" condition, prior to significant modem anthropogenic influence, and in its contemporary condition. The pre-development system model was calibrated by varying marsh plain elevations in order to match sparse observations of tidal characteristics; the contemporary system model was calibrated to observed flow, stage, and salinity data. A recent three-year period covering a wide range of flow conditions was used to compare and contrast the hydrodynamic behavior of the two systems. While the contemporary model simulation assumed historical observed boundary conditions, the pre-development model simulation assumed conditions thought to exist prior to the alterations of the past two centuries. The relationship between estuary outflow and the longitudinal distance from the estuary mouth to the 2 psu bottom salinity isohaline (X2) was analyzed. Salt intrusion in the pre-development system was found to be slightly more sensitive to outflow and responded faster to changes in outflow than in the contemporary system. Changes in estuary outflows were responsible for more of the salt intrusion differences between the two systems than were changes in estuary geometry and bathymetry. An analysis of the physical mechanisms contributing to salt intrusion found tidal trapping and other unsteady processes to be more important in the pre-development estuary than in the contemporary one. In both systems, steady processes such as estuarine circulation were strongest during neap tides and unsteady salt intrusion processes were strongest during spring tides, resulting in limited spring-neap variability in salt intrusion.