Salinity in the San Francisco Bay Estuary almost always experiences its yearly maximum during late summer, but climate variability produces marked interannual variations. The atmospheric circulation pattern impacts the estuary primarily through variations of runoff from rainfall and snowmelt from the Sierra Nevada and, secondarily, through variations in the near-surface salinity in the coastal ocean. While winter precipitation is the primary influence upon salinity in the estuary, spring climate variations also contribute importantly to salinity fluctuations. Spring atmospheric circulation influences both the magnitude and the timing of freshwater flows, through anomalies of precipitation and temperature. To help discriminate between the effects of these two influences, the record is divided into subsets according to whether spring conditions in the region are cool and wet, warm and wet, cool and dry, or warm and dry. Warm springs promote early snowmelt-driven flows, and cool springs result in delayed flows. In addition to effects of winter and spring climate variability operating on the watershed, there are more subtle effects that are transmitted into the estuary from the coastal ocean. These influences are most pronounced in cool and dry springs with low SS in the coastal ocean. A transect of SS records at stations from the mouth to the head of the bay suggests that the coastal ocean anomaly signal is attenuated from the mouth to the interior of the estuary. In contrast, a delayed, postsummer signal caused by winter and spring runoff variations from the upstream watershed are most pronounced at the head of the estuary and attenuate toward the mouth.