Foraminifera are ecosystem indicators and a source of paleoenvironmental proxy data across marine systems worldwide. Differences in size fraction selection among paleoenvironmental studies may influence assemblage composition and environmental interpretations, yet few studies have evaluated these effects in estuarine settings. This study quantifies and compares benthic foraminiferal assemblages from estuarine sediments across two size fractions: 63–150μm and 150-250μm. Sediment cores were collected in the San Francisco Bay Estuary as part of a study to characterize the sedimentology and stratigraphy of the bay; here we focus on sediments from core J190SF-90-24 (6.1m water depth). Benthic foraminiferal assemblages from a suite of representative intervals were analyzed to evaluate the influence of size fraction selection on paleoenvironmental interpretations. Assemblage composition, biodiversity indices, multivariate analyses, and the resulting Ammonia–Elphidium (A–E) Index values are compared between the two size fractions to assess their influence on paleoenvironmental interpretation. Standardizing the sampling procedure for estuarine fossil foraminiferal studies will enable researchers to compare results across studies and allow for a more robust understanding of estuarine systems through time.