Physical, Biological, and Management Responses to Variable Freshwater Flow into the San Francisco Estuary

Freshwater flow is the principal cause of physical variability in estuaries and a focus of conflict in estuaries where a substantial fraction of the freshwater is diverted. Variation in freshwater flow can have many effects: inundation of flood plains, increase loading and advective transport of materials and organisms, dilution or mobilization of contaminants, compression of the estuarine salinity field and density gradient, increase in stratification, and decrease in residence time for water while increasing it for some particles and biota. In the San Francisco Estuary, freshwater flow is highly variable, and has been altered by shifts in seasonal patterns of river flow and increases in diversions from tidal and non-tidal regions, entraining fish of several species of concern. Abundance or survival of several estuarine-dependent species also increases with freshwater outflow. These relationships to flow may be due to several potential mechanisms, each with its own locus and period of effectiveness, but no mechanism has been conclusively shown to underlie the flow relationship of any species. Several flow-based management actions were established in the mid-1990s, including a salinity standard based on these flow effects, as well as reductions in diversion pumping during critical periods for listed species of fish. The effectiveness of these actions has not been established. To make the salinity standard more effective and more applicable to future estuarine conditions will require investigation to determine the underlying mechanisms. Effects of entrainment at diversion facilities are more straightforward conceptually but difficult to quantify, and resolving these may require experimental manipulations of diversion flow.