A 3.5-m gravity core (DJ6-93SF-6) from San Francisco Bay reveals a complex paleoclimatic history of the region over the last 3870 cal YBP. A polynomial equation based on 11 AMS ¹⁴C ages provides an excellent age model for the core, and environmental proxies for water temperature and salinity are derived from various foraminiferal abundances, stable carbon and oxygen isotopes, and Mg/Ca ratios. Two foraminiferal associations were identified by Q-mode cluster analysis: a colder-water Elphidium excavatum association and the warmer-water Ammonia beccarii–Elphidium gunteri association. The E. excavatum association dominates the core for all but about 600 years out of the last four millennia.

At 3870 cal YBP, water temperatures were warm (13.9°C) and freshwater inflow was reduced compared with today. From 3590 to 2860 cal YBP, temperatures dropped 0.5°C and the climate remained dry. This was followed by a period of pronounced lower δ¹³C values, indicating that conditions became considerably wetter from 2860 to 2170 cal YBP. During this interval, the temperature oscillated frequently, peaking at 13.9°C at 2710 cal YBP, then dropping shortly thereafter to 12.8°C at 2420 cal YBP. Freshwater inflow gradually decreased between 2170 and 1950 cal YBP with a minimal rise in temperature, then changed quickly to colder and wetter conditions at 1900 cal YBP. Drier conditions then prevailed until 1480 cal YBP with water temperatures fluctuating between 13.1°C and 13.8°C, followed by wetter climate from 1480 to 1320 cal YBP.

A significant faunal shift from the E. excavatum association to the A. beccarii–E. gunteri association occurred from 1250 to 650 cal YBP, possibly due to regional warming, decreased oxygen availability, and/or a change in the phytoplankton community. Associated with this change in faunal composition were warm and dry conditions, representative of the Medieval Warm Period (Medieval Climatic Anomaly). A climatic shift coincident with the onset of the Little Ice Age (LIA I and LIA II) is evident from 650 to 280 cal YBP, with the return of the E. excavatum association and an extreme drop in δ¹⁸O values, all indicating increased precipitation and fresh water inflow. This was followed by generally drier conditions to the present, except for a brief wet period around 100 cal YBP, and fairly consistent water temperatures in the middle 13°C, except for a drop to 12.8°C at 200 cal YBP.

Two significant faunal changes occur near the top of the core. First, there is the reappearance of the A. beccarii–E. gunteri association, suggesting that, once again, regional warming has taken place, oxygen availability has declined, and/or environmental conditions changed such that diatoms have become a scarce food source. Second, there is the first appearance of the invasive Japanese foraminifera Trochammina hadai Uchio, a species that commonly lives in highly polluted areas and is an indicator of eutrophication in its native estuaries. At the same time, freshwater inflow decreased, which may be explained by global warming during the last 100 years, or more likely due to modern water diversion for agriculture in the central valley of California.