Fossil foraminifers (Elphidium excavatum forma selseyensis) recovered from a sediment core from the San Francisco Bay are analyzed for their oxygen isotopic composition. About 8 m of core believed to represent the first 600 years of the current (Holocene) bay's existence at the sample site (from approximately 7650–7050 cal YBP) are highlighted here. This record, deposited at a high, uniform accumulation rate, shows pronounced variation in measured carbonate δ¹⁸O, including some of the highest values in the entire Holocene record at the site. It is proposed that this interval records a period during which the fundamental mixing dynamics of the modern estuary became established. We interpret the extremely high δ¹⁸O values at about 7400 cal YBP as being indicative of a strongly stratified estuary sampled below its halocline and argue that subsequent details of the isotope record suggest a gradual decrease in water column stratification until conditions qualitatively characteristic of the modern estuary are established about 7300 cal YBP.