Records of stable carbon isotopes (δ13C) are presented from cores collected from four San Francisco Bay marshes and used as a proxy for changes in estuary salinity. The δ13C value of organic marsh sediments are a reflection of the relative proportion of C3 vs. C4 plants occupying the surface, and can thus be used as a proxy for vegetation change on the marsh surface. The four marshes included in this study are located along a natural salinity gradient that exists in the San Francisco Bay, and records of vegetation change at all four sites can be used to infer changes in overall estuary paleosalinity. The δ13C values complement pollen data from the same marsh sites producing a paleoclimate record for the late Holocene period in the San Francisco Bay estuary. The data indicate that there have been periods of higher-than-average salinity in the Bay estuary (reduced fresh water inflow), including 1600–1300 cal yr B.P., 1000–800 cal yr B.P., 300–200 cal yr B.P., and ca. A.D. 1950 to the present. Periods of lower-than-average salinity (increased fresh water inflow) occurred before 2000 cal yr B.P., from 1300 to 1200 cal yr B.P. and ca. 150 cal yr B.P. to A.D. 1950. A comparison of the timing of these events with records from the California coast, watershed, and beyond the larger drainage of the Bay reveals that the paleosalinity variations reflected regional precipitation.