The distribution of foraminifera in most of San Francisco Bay is well documented, but this is not the case for the subembayment known as Central Bay. To resolve this, 55 grab samples obtained in 1998 were analyzed to characterize the foraminiferal fauna in the surface sediments of the area. Thirty-five species were identified, including the invasive Japanese species Trochammina hadai that was introduced into the bay in the early 1980s. A cluster analysis of the samples from Central Bay produced three groups (biofacies) and one outlier. The Shallow Subtidal Biofacies is characterized by a marsh to shallow-subtidal agglutinated fauna, dominated by T. hadai but also including T. inflata, T. macrescens, Haplophragmoides subinvolutum, and Miliammina fusca. The Intermediate Subtidal Biofacies, the Intermediate Subtidal Outlier, and the Deep Subtidal Biofacies are dominated by calcareous taxa, most notably Ammonia tepida, Elphidium excavatum, and Elphidiella hannai. Ammonia tepida is most abundant in the warmer, intermediate depths of eastern Central Bay, abundances of E. excavatum peak in the cooler estuarine water near Alcatraz Island, and E. hannai thrives in the cold water west of Angel Island in a transitional setting between the deep subtidal estuarine and the nearshore marine environments. The recovery of oceanic species as far east as Angel Island indicate that western Central Bay is the most marine-influenced region of San Francisco Bay.

Samples collected from 1965 onward were also compared with those from 1998 to investigate how the distribution of benthic foraminifera in Central Bay has changed over the latter half of the 20th Century, particularly in response to the invasion by Trochammina hadai. In 1998, T. hadai was recovered at 46 of 55 sites in Central Bay, comprising from 0.3 to 97% (mean = 23%) of the foraminiferal fauna. With the species’ affiliation for shallow environments, it is not unexpected that it dominated the fauna of the Shallow Subtidal Biofacies (68-97%, mean = 77%) and was also a significant component of the Intermediate Subtidal Biofacies (7-51%, averaging 28%). In the deeper waters west of Alcatraz Island, the abundance of T. hadai was significantly less (mean = 8%), most likely reflecting allochthonous specimens that were the result of post-mortem transport. A cluster analysis clearly distinguishes pre- and post-invasion biofacies, illustrating how dominant T. hadai has become in Central Bay.